Genetically modified major histocompatibility complex mice

ABSTRACT

The invention provides genetically modified non-human animals that express chimeric human/non-human MHC I and MHC II polypeptides and/or human or humanized β2 microglobulin polypeptide, as well as embryos, cells, and tissues comprising the same. Also provided are constructs for making said genetically modified animals and methods of making the same. Methods of using the genetically modified animals to study various aspects of human immune system are provided.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims benefit under 35 U.S.C. §119(e) of U.S.provisional patent application Ser. No. 62/039,333, filed Aug. 19, 2014and is a continuation-in-part application of U.S. application Ser. No.14/185,316, filed Feb. 20, 2014, which claims the benefit under 35§119(e) of U.S. Provisional Patent Application Ser. No. 61/767,811,filed Feb. 22, 2013, all of which are hereby incorporated by referencein their entirety.

FIELD OF THE INVENTION

The present invention relates to a genetically modified non-humananimal, e.g., a rodent (e.g., a mouse or a rat), that expresses a humanor humanized Major Histocompatibility Complex (MHC) class I and a humanor humanized MHC class II molecules. The invention also relates to agenetically modified non-human animal, e.g., a mouse or a rat, thatexpresses a human or humanized MHC I protein (e.g., MHC I α chain) and ahuman or humanized MHC II protein (e.g., MHC II α and MHC II β chains),and further expresses a human or humanized β2 microglobulin; as well asembryos, tissues, and cells expressing the same. The invention furtherprovides methods for making a genetically modified non-human animal thatexpresses both human or humanized MHC class I and class II proteins,and/or β2 microglobulin. Also provided are methods for identifying andevaluating peptides in the context of a humanized cellular immune systemin vitro or in a genetically modified non-human animal, and methods ofmodifying an MHC locus of a non-human animal, e.g., a mouse or a rat, toexpress a human or humanized MHC I and a human or humanized MHC IIproteins.

BACKGROUND OF THE INVENTION

In the adaptive immune response, foreign antigens are recognized byreceptor molecules on B lymphocytes (e.g., immunoglobulins) and Tlymphocytes (e.g., T cell receptor or TCR). These foreign antigens arepresented on the surface of cells as peptide fragments by specializedproteins, generically referred to as major histocompatibility complex(MHC) molecules. MHC molecules are encoded by multiple loci that arefound as a linked cluster of genes that spans about 4 Mb. In mice, theMHC genes are found on chromosome 17, and for historical reasons arereferred to as the histocompatibility 2 (H-2) genes. In humans, thegenes are found on chromosome 6 and are called human leukocyte antigen(HLA) genes. The loci in mice and humans are polygenic; they includethree highly polymorphic classes of MHC genes (class I, II and III) thatexhibit similar organization in human and murine genomes (see FIG. 2 andFIG. 3, respectively).

MHC loci exhibit the highest polymorphism in the genome; some genes arerepresented by >300 alleles (e.g., human HLA-DRβ and human HLA-B). Allclass I and II MHC genes can present peptide fragments, but each geneexpresses a protein with different binding characteristics, reflectingpolymorphisms and allelic variants. Any given individual has a uniquerange of peptide fragments that can be presented on the cell surface toB and T cells in the course of an immune response.

Both humans and mice have class I MHC genes (see FIG. 2 and FIG. 3,respectively). In humans, the classical class I genes are termed HLA-A,HLA-B and HLA-C, whereas in mice they are H-2K, H-2D and H-2L. Class Imolecules consist of two chains: a polymorphic α-chain (sometimesreferred to as heavy chain) and a smaller chain called β2-microglobulin(also known as light chain), which is generally not polymorphic (FIG. 1,left). These two chains form a non-covalent heterodimer on the cellsurface. The α-chain contains three domains (α1, α2 and α3). Exon 1 ofthe α-chain gene encodes the leader sequence, exons 2 and 3 encode theα1 and α2 domains, exon 4 encodes the α3 domain, exon 5 encodes thetransmembrane domain, and exons 6 and 7 encode the cytoplasmic tail. Theα-chain forms a peptide-binding cleft involving the α1 and α2 domains(which resemble Ig-like domains) followed by the α3 domain, which issimilar to β2-microglobulin.

β2 microglobulin is a non-glycosylated 12 kDa protein; one of itsfunctions is to stabilize the MHC class I α-chain. Unlike the α-chain,the β2 microglobulin does not span the membrane. The human β2microglobulin locus is on chromosome 15, while the mouse locus is onchromosome 2. The β2 microglobulin gene consists of 4 exons and 3introns. Circulating forms of β2 microglobulin are present in serum,urine, and other body fluids; non-covalently MHC I-associated β2microglobulin can be exchanged with circulating β2 microglobulin underphysiological conditions.

Class I MHC molecules are expressed on all nucleated cells, includingtumor cells. They are expressed specifically on T and B lymphocytes,macrophages, dendritic cells and neutrophils, among other cells, andfunction to display peptide fragments (typically 8-10 amino acids inlength) on the surface to CD8+ cytotoxic T lymphocytes (CTLs). CTLs arespecialized to kill any cell that bears an MHC I-bound peptiderecognized by its own membrane-bound TCR. When a cell displays peptidesderived from cellular proteins not normally present (e.g., of viral,tumor, or other non-self origin), such peptides are recognized by CTLs,which become activated and kill the cell displaying the peptide.

Both humans and mice also have class II MHC genes (see FIGS. 2 and 3,respectively). In humans, the classical MHC II genes are termed HLA-DP,HLA-DQ, and HLA-DR, whereas in mice they are H-2A and H-2E (oftenabbreviated as I-A and I-E, respectively). Additional proteins encodedby genes in the MHC II locus, HLA-DM and HLA-DO in humans, and H-2M andH-2O in mice, are not found on the cell surface, but reside in theendocytic compartment and ensure proper loading of MHC II molecules withpeptides. Class II molecules consist of two polypeptide chains: α chainand β chain. The extracellular portion of the α chain contains twoextracellular domains, α1 and α2; and the extracellular portion of the βchain also contains two extracellular domains, β1 and β2 (see FIG. 1,right). The α and the β chains are non-covalently associated with eachother.

MHC class II molecules are expressed on antigen-presenting cells (APCs),e.g., B cells, macrophages, dendritic cells, endothelial cells during acourse of inflammation, etc. MHC II molecules expressed on the surfaceof APCs typically present antigens generated in intracellular vesiclesto CD4+T cells. In order to participate in CD4+T cell engagement, theMHC class II complex with the antigen of interest must be sufficientlystable to survive long enough to engage a CD4+T cell. When a CD4+Thelper cell is engaged by a foreign peptide/MHC II complex on thesurface of APC, the T cell is activated to release cytokines that assistin immune response to the invader.

Not all antigens will provoke T cell activation due to tolerancemechanisms. However, in some diseases (e.g., cancer, autoimmunediseases) peptides derived from self-proteins become the target of thecellular component of the immune system, which results in destruction ofcells presenting such peptides. There has been significant advancementin recognizing antigens that are clinically significant (e.g., antigensassociated with various types of cancer). However, in order to improveidentification and selection of peptides that will provoke a suitableresponse in a human T cell, in particular for peptides of clinicallysignificant antigens, there remains a need for in vivo and in vitrosystems that mimic aspects of human immune system. Thus, there is a needfor biological systems (e.g., genetically modified non-human animals andcells) that can display components of a human immune system.

SUMMARY OF THE INVENTION

A biological system for generating or identifying peptides thatassociate with human MHC class I proteins and chimeras thereof and bindCD8+T cells, as well as peptides that associate with human MHC class IIproteins and chimeras thereof and bind to CD4+T cells, is provided.Non-human animals comprising non-human cells that express humanizedmolecules that function in the cellular immune response are provided.Humanized rodent loci that encode humanized MHC I and MHC II proteinsare also provided. Humanized rodent cells that express humanized MHCmolecules are also provided. In vivo and in vitro systems are providedthat comprise humanized rodent cells, wherein the rodent cells expressone or more humanized immune system molecules.

In various embodiments, provided herein is a non-human animal comprisingat an endogenous MHC locus a first nucleotide sequence encoding achimeric human/non-human MHC I polypeptide, wherein a human portion ofthe chimeric MHC I polypeptide comprises an extracellular domain of ahuman MHC I polypeptide; a second nucleotide sequence encoding achimeric human/non-human MHC II α polypeptide, wherein a human portionof the chimeric human/non-human MHC II α polypeptide comprises anextracellular domain of a human MHC II α polypeptide; and a thirdnucleotide sequence encoding a chimeric human/non-human MHC II βpolypeptide, wherein a human portion of the chimeric human/non-human MHCII β polypeptide comprises an extracellular domain of a human MHC II βpolypeptide, wherein the non-human animal expresses functional chimerichuman/non-human MHC I and MHC II proteins from its endogenous non-humanMHC loci. In one embodiment, the animal does not express functionalendogenous MHC I, II α, and/or II β polypeptides from the endogenousnon-human MHC loci. In some embodiments, the animal is not capable ofexpressing functional endogenous MHC I, II α, and/or II β polypeptides,since for example, genes encoding endogenous MHC I and MHC II proteinsmay be functionally inactivated, e.g., are incapable of beingtranscribed and translated into endogenous MHC I and MHC II proteins,respectively. In various embodiments, all endogenous genes of thenon-human animal encoding MHC molecules that are expressed on the cellsurface (e.g., present antigen to and associate with T cell receptor)are functionally inactivated such that the animal does not expressendogenous cell-surface MHC I, II α, and/or II β polypeptides. In someembodiments, genes may be functionally inactivated with a mutation(e.g., inversion), replacement of the gene (in whole or in part) and/ordeletion of the gene (in whole or in part). In some embodiments, anon-human MHC class I gene may be functionally inactivated by thereplacement of an endogenous sequence encoding α1, α2, and α3 domains ofan endogenous MHC class I polypeptide with a sequence encoding α1, α2,and α3 domains of a human MHC class I polypeptide; a non-human MHC classII α gene may be inactivated by the replacement of an endogenoussequence encoding α1 and α2 domains of an endogenous MHC class II αpolypeptide with a sequence encoding α1 and α2 domains of a human MHCclass II α polypeptide; or a non-human MHC class II β gene may beinactivated by the replacement of an endogenous sequence encoding β1 andβ2 domains of an endogenous MHC class II β polypeptide with a sequenceencoding β1 and β2 domains of a human MHC class II β polypeptide.

In one aspect, the first nucleotide sequence is located at theendogenous non-human MHC I locus, the second nucleotide sequence islocated at the endogenous non-human MHC II α locus, and the thirdnucleotide sequence is located at the endogenous non-human MHC II βlocus. In one aspect, the first, second and/or third nucleotidesequence(s) are operably linked to endogenous non-human regulatoryelements. In one aspect, the first nucleotide sequence is operablylinked to endogenous non-human MHC I promoter and regulatory elements,the second nucleotide sequence is operably linked to endogenousnon-human MHC II α promoter and regulatory elements, and the thirdnucleotide sequence is operably linked to endogenous non-human MHC II βpromoter and regulatory elements.

In one embodiment, the human portion of a chimeric MHC I polypeptidecomprises α1, α2, and α3 domains of the human MHC I polypeptide. In oneaspect, a non-human portion of the chimeric MHC I polypeptide comprisestransmembrane and cytoplasmic domains of an endogenous non-human MHC Ipolypeptide. The human MHC I polypeptide may be selected from the groupconsisting of HLA-A, HLA-B, and HLA-C. In one embodiment, the human MHCI polypeptide is HLA-A2. In another aspect, the human MHC I polypeptideis HLA-A3, HLA-B7, HLA-B27, HLA-Cw6, or any other MHC I moleculeexpressed in a human population. In an additional embodiment, anon-human animal of the invention further comprises at its endogenousnon-human β2 microglobulin locus a nucleotide sequence encoding a humanor humanized β2 microglobulin polypeptide, wherein the animal expressesthe human or humanized β2 microglobulin polypeptide.

In one embodiment, the human MHC II α extracellular domain compriseshuman MHC II α1 and α2 domains. In another embodiment, the human MHC IIβ extracellular domain comprises human MHC II β1 and β2 domains. In oneaspect, the non-human portion of a chimeric human/non-human MHC II αpolypeptide comprises transmembrane and cytoplasmic domains of anendogenous non-human MHC II α polypeptide. In one aspect, the non-humanportion of a chimeric human/non-human MHC II β polypeptide comprisestransmembrane and cytoplasmic domains of an endogenous non-human MHC IIβ polypeptide. In one embodiment, the human portions of a chimerichuman/mouse MHC II α and β polypeptides are derived from a human HLAclass II protein selected from the group consisting of HLA-DR, HLA-DQ,and HLA-DP. In one specific embodiment, the human portions of chimerichuman/non-human MHC II α and β polypeptides are derived from a humanHLA-DR2 protein. Alternatively, the human portions of chimerichuman/non-human MHC II α and β polypeptides may be derived from humanMHC II protein selected from HLA-DR4, HLA-DQ2.5, HLA-DQ8, or any otherMHC II molecule expressed in a human population.

In some aspects, a provided animal comprises two copies of the MHC locuscontaining the first, the second, and the third nucleotide sequences,while in other aspects, a provided animal comprises one copy of the MHClocus containing the first, the second, and the third nucleotidesequences. Thus, the animal may be homozygous or heterozygous for theMHC locus containing nucleotide sequences encoding chimerichuman/non-human MHC I, MHC II α, and MHC II β polypeptides. In someembodiments of the invention, the genetically modified MHC locus,comprising nucleotide sequences encoding chimeric human/non-human MHC I,MHC II α, and MHC II β polypeptides described herein, is in the germlineof the non-human animal.

Also provided herein is an MHC locus comprising a first nucleotidesequence encoding a chimeric human/non-human MHC I polypeptide, whereina human portion of the chimeric MHC I polypeptide comprises anextracellular domain of a human MHC I polypeptide; a second nucleotidesequence encoding a chimeric human/non-human MHC II α polypeptide,wherein a human portion of the chimeric human/non-human MHC II αpolypeptide comprises an extracellular domain of a human MHC II αpolypeptide; and a third nucleotide sequence encoding a chimerichuman/non-human MHC II β polypeptide, wherein a human portion of thechimeric human/non-human MHC II β polypeptide comprises an extracellulardomain of a human MHC II β polypeptide. In some aspects, non-humanportions of the chimeric MHC I, II α, and II β polypeptides comprisetransmembrane and cytoplasmic domains of non-human MHC I, II α, and IIβ, respectively.

In one embodiment, the genetically engineered non-human animal is arodent. In one embodiment, the rodent is a rat or a mouse. In oneembodiment, the rodent is a mouse. Thus, in one aspect, the firstnucleotide sequence encodes a chimeric human/mouse MHC I polypeptide,and the mouse portion of the chimeric MHC I polypeptide is derived fromH-2K, H-2D, or H-2L. In one specific embodiment, the mouse portion ofthe chimeric MHC I polypeptide is derived from H-2K. In one aspect, thesecond nucleotide sequence encodes a chimeric human/mouse MHC II αpolypeptide, the third nucleotide sequence encodes a chimerichuman/mouse MHC II β polypeptide, and the mouse portions of the chimericMHC II α and β polypeptides are derived from H-2E or H-2A. In yetanother embodiment, the mouse does not express any functional endogenousMHC II α and MHC II β polypeptides on a cell surface, and the only MHCII α and MHC II β polypeptides expressed on a cell surface are chimerichuman/mouse MHC II α and MHC II β polypeptides. In a specificembodiment, the mouse portions of the chimeric MHC II polypeptides arederived from H-2E. In some embodiments, the mouse does not expressfunctional endogenous MHC polypeptides from its H-2D locus. In someembodiments, the mouse is engineered to lack all or a portion of anendogenous H-2D locus. In some embodiments, the mouse does not expressany endogenous MHC I and II polypeptides on a cell surface; in someembodiments, all endogenous mouse MHC I and II polypeptides that areexpressed on a cell surface are functionally inactivated or fully orpartially deleted.

Thus, also provided herein is a genetically engineered mouse comprisingat an endogenous MHC locus a first nucleotide sequence encoding achimeric human/mouse MHC I polypeptide, wherein the human portion of thechimeric MHC I polypeptide comprises an extracellular domain of a humanMHC I polypeptide; a second nucleotide sequence encoding a chimerichuman/mouse MHC II α polypeptide, wherein the human portion of thechimeric human/non-human MHC II α polypeptide comprises an extracellulardomain of a human MHC II α polypeptide; and a third nucleotide sequenceencoding a chimeric human/mouse MHC II β polypeptide, wherein the humanportion of the chimeric human/non-human MHC II β polypeptide comprisesan extracellular domain of a human MHC II β polypeptide; wherein themouse expresses functional chimeric human/mouse MHC I and MHC IIproteins from its endogenous mouse MHC locus. In one specificembodiment, the first nucleotide sequence encodes a chimeric HLA-A2/H-2Kpolypeptide, the second nucleotide sequence encodes an α chain of achimeric HLA-DR/H-2E polypeptide (e.g., HLA-DR2/H-2E polypeptide), andthe third nucleotide sequence encodes a β chain of a chimericHLA-DR/H-2E polypeptide (e.g., HLA-DR2/H-2E polypeptide), and the mouseexpresses functional HLA-A2/H-2K and HLA-DR/H-2E (e.g., HLA-DR2/H-2E)proteins. In an additional embodiment, the mouse further comprises at anendogenous β2 microglobulin locus a nucleotide sequence encoding a humanor humanized β2 microglobulin polypeptide. In one embodiment, the mousedoes not express functional endogenous MHC polypeptides from itsendogenous MHC locus. In some embodiments, the mouse does not expressfunctional MHC I or II polypeptides on a cell surface; in someembodiments, the only MHC I and MHC II polypeptides expressed on a cellsurface are chimeric human/mouse MHC I and II polypeptides. In someembodiments, the mouse does not express functional endogenous MHCpolypeptides from its H-2D locus. In some embodiments, the mouse isengineered to lack all or a portion of an endogenous H-2D locus. In yetanother embodiment, the endogenous H-2D is deleted or functionallyinactivated.

Also provided herein are methods for generating a genetically modifiednon-human animal (e.g., rodent, e.g., mouse or rat) described herein.Thus, in one aspect, the invention provides a method of generating agenetically modified non-human animal comprising replacing at anendogenous non-human MHC II locus a nucleotide sequence encoding anon-human MHC II complex with a nucleotide sequence encoding a chimerichuman/non-human MHC II complex to generate a first non-human animal; andreplacing at an endogenous non-human MHC I locus a nucleotide sequenceencoding a non-human MHC I polypeptide with a nucleotide sequenceencoding a chimeric human/non-human MHC I polypeptide to generate asecond non-human animal. In one aspect, the steps of replacingnucleotide sequences comprise homologous recombination in non-human EScells, and the second non-human animal is generated by homologousrecombination in ES cells bearing nucleotide sequences encoding chimerichuman/non-human MHC II complex. The chimeric MHC II complex compriseschimeric human/non-human MHC II α and β polypeptides. In someembodiments, ES cells are mouse ES cells engineered to lack all or aportion of an endogenous H-2D locus. In other embodiments, the ES cellsare engineered to have a functionally inactivated H-2D locus. In yetanother embodiments, the ES cells lack or are engineered to lack or havefunctional inactivation of all or a portion of endogenous H-2A, H-2E,H-2K, H-2D, and H-2L loci.

In an alternative embodiment, the invention provides a method ofgenerating a genetically modified non-human animal comprising replacingat an endogenous non-human MHC I locus a nucleotide sequence encoding anon-human MHC I polypeptide with a nucleotide sequence encoding achimeric human/non-human MHC I polypeptide to generate a first non-humananimal; and replacing at an endogenous non-human MHC II locus anucleotide sequence encoding a non-human MHC II complex with anucleotide sequence encoding a chimeric human/non-human MHC II complexto generate a second non-human animal. In one aspect, the steps ofreplacing nucleotide sequences comprise homologous recombination innon-human ES cells, and the second non-human animal is generated byhomologous recombination in ES cells bearing a nucleotide sequenceencoding chimeric human/non-human MHC I polypeptide.

Also provided herein are cells, e.g., isolated antigen-presenting cells,derived from the non-human animals (e.g., rodents, e.g., mice or rats)described herein. Tissues and embryos derived from the non-human animalsdescribed herein are also provided.

Any of the embodiments and aspects described herein can be used inconjunction with one another, unless otherwise indicated or apparentfrom the context. Other embodiments will become apparent to thoseskilled in the art from a review of the ensuing detailed description.The following detailed description includes exemplary representations ofvarious embodiments of the invention, which are not restrictive of theinvention as claimed. The accompanying figures constitute a part of thisspecification and, together with the description, serve only toillustrate embodiments and not to limit the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic drawing of the MHC I (left panel) and MHC II(right panel) class molecules expressed on the surface of a cell. Thegray circles represent peptides bound in the peptide-binding clefts.

FIG. 2 is a schematic representation (not to scale) of the relativegenomic structure of the human HLA, showing class I, II and III genes.

FIG. 3 is a schematic representation (not to scale) of the relativegenomic structure of the mouse MHC, showing class I, II and III genes.

FIG. 4 depicts the strategy for generating a humanized MHC locuscomprising humanized MHC I and MHC II genes. In the particularembodiment depicted, the MHC locus of the generated mouse compriseschimeric HLA-A2/H-2K and HLA-DR2/H-2E sequences (H2-K^(+/1666)MHC-II^(+/61 12)) and lacks H2-D sequence (H2-D^(+/delete)) and H-2Asequence (the genetic engineering scheme also results in a deletion ofH-2A, see Example 1.2). Large Targeting Vectors introduced into ES cellsat each stage of humanization are depicted to the right of the arrows.

FIG. 5 is a schematic diagram (not to scale) of the targeting strategyused for making a chimeric H-2K locus that expresses an extracellularregion of a human HLA-A2 protein. Mouse sequences are represented inblack and human sequences are represented in white. L=leader,UTR=untranslated region, TM=transmembrane domain, CYT=cytoplasmicdomain, HYG=hygromycin.

FIG. 6 is a schematic diagram of an exemplary HLA-DR2/H-2E largetargeting vector.

FIG. 7 is a schematic representation of exemplary genotypes of MHC loci(**) represents H-2L gene that is not present in all mouse strains),where endogenous mouse H-2K and H-2E loci were replaced by chimerichuman/mouse loci, and H-2A and H-2D loci were deleted.

FIG. 8 depicts contour plots of percentage of mouse CD3+T cells andCD19+B cells in spleens from 3 wild-type (WT) control mice and 3chimeric A2 and DR2 mice. Cells were gated on live cells discriminatedbased on FSC/SSC gating. HLA-A2/H-2K, HLA-DR2/H-2E, H-2A-del, H-2D-delHET*=mice created in the genetic engineering scheme depicted in FIG. 4,also referred to in this and remaining figures as “chimeric A2 and DR2mice.”

FIG. 9 depicts histograms of mouse MHC class I (H2D), human MHC class I(HLA-A2), and human MHC class II (HLA-DR) expression levels on CD19+Bcells from spleens of 3 wild-type (WT) control mice and 3 chimeric A2and DR2 mice.

FIG. 10 depicts histograms of mouse MHC class I (H2D), human MHC class I(HLA-A2), and human MHC class II (HLA-DR) expression levels on CD14+monocytes from spleens of 3 wild-type (WT) control mice and 3 chimericA2 and DR2 mice.

FIG. 11 depicts histograms of mouse MHC class I (H2D), human MHC class I(HLA-A2), and human MHC class II (HLA-DR) expression levels on CD3+Tcells from spleens of 3 wild-type (WT) control mice and 3 chimeric A2and DR2 mice.

DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION Definitions

The present invention provides genetically modified non-human animals(e.g., mice, rats, rabbits, etc.) that express both human or humanizedMHC I and MHC II proteins; embryos, cells, and tissues comprising thesame; methods of making the same; as well as methods of using the same.Unless defined otherwise, all terms and phrases used herein include themeanings that the terms and phrases have attained in the art, unless thecontrary is clearly indicated or clearly apparent from the context inwhich the term or phrase is used.

The term “conservative,” when used to describe a conservative amino acidsubstitution, includes substitution of an amino acid residue by anotheramino acid residue having a side chain R group with similar chemicalproperties (e.g., charge or hydrophobicity). Conservative amino acidsubstitutions may be achieved by modifying a nucleotide sequence so asto introduce a nucleotide change that will encode the conservativesubstitution. In general, a conservative amino acid substitution willnot substantially change the functional properties of interest of aprotein, for example, the ability of MHC I or MHC II to present apeptide of interest. Examples of groups of amino acids that have sidechains with similar chemical properties include aliphatic side chainssuch as glycine, alanine, valine, leucine, and isoleucine;aliphatic-hydroxyl side chains such as serine and threonine;amide-containing side chains such as asparagine and glutamine; aromaticside chains such as phenylalanine, tyrosine, and tryptophan; basic sidechains such as lysine, arginine, and histidine; acidic side chains suchas aspartic acid and glutamic acid; and, sulfur-containing side chainssuch as cysteine and methionine. Conservative amino acids substitutiongroups include, for example, valine/leucine/isoleucine,phenylalanine/tyrosine, lysine/arginine, alanine/valine,glutamate/aspartate, and asparagine/glutamine. In some embodiments, aconservative amino acid substitution can be a substitution of any nativeresidue in a protein with alanine, as used in, for example, alaninescanning mutagenesis. In some embodiments, a conservative substitutionis made that has a positive value in the PAM250 log-likelihood matrixdisclosed in Gonnet et al. ((1992) Exhaustive Matching of the EntireProtein Sequence Database, Science 256:1443-45), hereby incorporated byreference. In some embodiments, the substitution is a moderatelyconservative substitution wherein the substitution has a nonnegativevalue in the PAM250 log-likelihood matrix.

Thus, also encompassed by the invention is a genetically modifiednon-human animal whose genome comprises a nucleotide sequence encoding ahuman or humanized MHC I and II polypeptides, wherein MHC I or MHC IIthe polypeptide comprises conservative amino acid substitutions in theamino acid sequence described herein.

One skilled in the art would understand that in addition to the nucleicacid residues encoding a human or humanized MHC I or MHC II polypeptidedescribed herein, due to the degeneracy of the genetic code, othernucleic acids may encode the polypeptide of the invention. Therefore, inaddition to a genetically modified non-human animal that comprises inits genome a nucleotide sequence encoding MHC I and MHC II polypeptideswith conservative amino acid substitutions, a non-human animal whosegenome comprises a nucleotide sequence that differs from that describedherein due to the degeneracy of the genetic code is also provided.

The term “identity” when used in connection with sequence includesidentity as determined by a number of different algorithms known in theart that can be used to measure nucleotide and/or amino acid sequenceidentity. In some embodiments described herein, identities aredetermined using a ClustalW v. 1.83 (slow) alignment employing an opengap penalty of 10.0, an extend gap penalty of 0.1, and using a Gonnetsimilarity matrix (MacVector™ 10.0.2, MacVector Inc., 2008). The lengthof the sequences compared with respect to identity of sequences willdepend upon the particular sequences. In various embodiments, identityis determined by comparing the sequence of a mature protein from itsN-terminal to its C-terminal. In various embodiments when comparing achimeric human/non-human sequence to a human sequence, the human portionof the chimeric human/non-human sequence (but not the non-human portion)is used in making a comparison for the purpose of ascertaining a levelof identity between a human sequence and a human portion of a chimerichuman/non-human sequence (e.g., comparing a human ectodomain of achimeric human/mouse protein to a human ectodomain of a human protein).

The terms “homology” or “homologous” in reference to sequences, e.g.,nucleotide or amino acid sequences, means two sequences which, uponoptimal alignment and comparison, are identical in at least about 75% ofnucleotides or amino acids, e.g., at least about 80% of nucleotides oramino acids, e.g., at least about 90-95% nucleotides or amino acids,e.g., greater than 97% nucleotides or amino acids. One skilled in theart would understand that, for optimal gene targeting, the targetingconstruct should contain arms homologous to endogenous DNA sequences(i.e., “homology arms”); thus, homologous recombination can occurbetween the targeting construct and the targeted endogenous sequence.

The term “operably linked” refers to a juxtaposition wherein thecomponents so described are in a relationship permitting them tofunction in their intended manner. As such, a nucleic acid sequenceencoding a protein may be operably linked to regulatory sequences (e.g.,promoter, enhancer, silencer sequence, etc.) so as to retain propertranscriptional regulation. In addition, various portions of thechimeric or humanized protein of the invention may be operably linked toretain proper folding, processing, targeting, expression, and otherfunctional properties of the protein in the cell. Unless statedotherwise, various domains of the chimeric or humanized protein of theinvention are operably linked to each other.

The term “MHC I complex” or the like, as used herein, includes thecomplex between the MHC I α chain polypeptide and the β2-microglobulinpolypeptide. The term “MHC I polypeptide” or the like, as used herein,includes the MHC I α chain polypeptide alone. The terms “MHC IIcomplex,” “MHC II protein,” or the like, as used herein, include thecomplex between an MHC II α polypeptide and an MHC II β polypeptide. Theterm “MHC II α polypeptide” or “MHC II β polypeptide” (or the like), asused herein, includes the MHC II α polypeptide alone or MHC II βpolypeptide alone, respectively. Similarly, the terms “HLA-DR4 complex”,“HLA-DR4 protein,” “H-2E complex,” “H-2E” protein,” or the like, referto complex between α and β polypeptides. Typically, the terms “humanMHC” and “HLA” are used interchangeably.

The term “replacement” in reference to gene replacement refers toplacing exogenous genetic material at an endogenous genetic locus,thereby replacing all or a portion of the endogenous gene with anorthologous or homologous nucleic acid sequence. As demonstrated in theExamples below, nucleic acid sequence of endogenous MHC locus wasreplaced by a nucleotide sequence comprising sequences encoding aportion of human MHC I polypeptide, specifically, encoding theextracellular portion of the MHC I polypeptide; as well as portions ofhuman MHC II α and β polypeptides, specifically, encoding theextracellular portions of the MHC II α and β polypeptides.

“Functional” as used herein, e.g., in reference to a functionalpolypeptide, refers to a polypeptide that retains at least onebiological activity normally associated with the native protein. Forexample, in some embodiments of the invention, a replacement at anendogenous locus (e.g., replacement at an endogenous non-human MHClocus) results in a locus that fails to express a functional endogenouspolypeptide, e.g., MHC I or MHC II polypeptide. Likewise, the term“functional” as used herein in reference to functional extracellulardomain of a protein, refers to an extracellular domain that retains itsfunctionality, e.g., in the case of MHC I or MHC II, ability to bind anantigen, ability to bind a T cell co-receptor, etc. In reference togenes, an endogenous gene may be functionally inactivated by varioustechniques such that the whole gene or a portion of the gene thatencodes an endogenous protein is still present at its locus but the geneis incapable of encoding an endogenous protein that is biologicallyactive. In some embodiments of the invention, a replacement at theendogenous MHC locus results in a locus that fails to express anextracellular domain (e.g., a functional extracellular domain) of anendogenous MHC while expressing an extracellular domain (e.g., afunctional extracellular domain) of a human MHC.

Genetically Modified MHC Animals

In various embodiments, the invention generally provides geneticallymodified non-human animals that comprise in their genome a nucleotidesequence encoding a human or humanized MHC I and MHC II polypeptides;thus, the animals express a human or humanized MHC I and MHC IIpolypeptides.

MHC genes are categorized into three classes: class I, class II, andclass III, all of which are encoded either on human chromosome 6 ormouse chromosome 17. A schematic of the relative organization of thehuman and mouse MHC classes is presented in FIGS. 2 and 3, respectively.The MHC genes are among the most polymorphic genes of the mouse andhuman genomes. MHC polymorphisms are presumed to be important inproviding evolutionary advantage; changes in sequence can result indifferences in peptide binding that allow for better presentation ofpathogens to cytotoxic T cells.

MHC class I protein comprises an extracellular domain (which comprisesthree domains: α₁, α₂, and α₃), a transmembrane domain, and acytoplasmic tail. The α₁ and α₂ domains form the peptide-binding cleft,while the α₃ interacts with β2-microglobulin.

In addition to its interaction with β2-microglobulin, the α₃ domaininteracts with the TCR co-receptor CD8, facilitating antigen-specificactivation. Although binding of MHC class I to CD8 is about 100-foldweaker than binding of TCR to MHC class I, CD8 binding enhances theaffinity of TCR binding. Wooldridge et al. (2010) MHC Class I Moleculeswith Superenhanced CD8 Binding Properties Bypass the Requirement forCognate TCR Recognition and Nonspecifically Activate CTLs, J. Immunol.184:3357-3366. Interestingly, increasing MHC class I binding to CD8abrogated antigen specificity in CTL activation. Id.

CD8 binding to MHC class I molecules is species-specific; the mousehomolog of CD8, Lyt-2, was shown to bind H-2D^(d) molecules at the α3domain, but it did not bind HLA-A molecules. Connolly et al. (1988) TheLyt-2 Molecule Recognizes Residues in the Class I α3 Domain inAllogeneic Cytotoxic T Cell Responses, J. Exp. Med. 168:325-341.Differential binding was presumably due to CDR-like determinants (CDR1-and CDR2-like) on CD8 that was not conserved between humans and mice.Sanders et al. (1991) Mutations in CD8 that Affect Interactions with HLAClass I and Monoclonal Anti-CD8 Antibodies, J. Exp. Med. 174:371-379;Vitiello et al. (1991) Analysis of the HLA-restricted Influenza-specificCytotoxic T Lymphocyte Response in Transgenic Mice Carrying a ChimericHuman-Mouse Class I Major Histocompatibility Complex, J. Exp. Med.173:1007-1015; and, Gao et al. (1997) Crystal structure of the complexbetween human CD8αα and HLA-A2, Nature 387:630-634. It has been reportedthat CD8 binds HLA-A2 in a conserved region of the α3 domain (atposition 223-229). A single substitution (V245A) in HLA-A reducedbinding of CD8 to HLA-A, with a concomitant large reduction in Tcell-mediated lysis. Salter et al. (1989), Polymorphism in the α3 domainof HLA-A molecules affects binding to CD8, Nature 338:345-348. Ingeneral, polymorphism in the α3 domain of HLA-A molecules also affectedbinding to CD8. Id. In mice, amino acid substitution at residue 227 inH-2D^(d) affected the binding of mouse Lyt-2 to H-2D^(d), and cellstransfected with a mutant H-2D^(d) were not lysed by CD8+T cells. Potteret al. (1989) Substitution at residue 227 of H-2 class I moleculesabrogates recognition by CD8-dependent, but not CD8-independent,cytotoxic T lymphocytes, Nature 337:73-75.

Therefore, due to species specificity of interaction between the MHCclass I α3 domain and CD8, an MHC I complex comprising a replacement ofan H-2K α3 domain with a human HLA-A2 α3 domain was nonfunctional in amouse (i.e., in vivo) in the absence of a human CD8. In animalstransgenic for HLA-A2, substitution of human α3 domain for the mouse α3domain resulted in restoration of T cell response. Irwin et al. (1989)Species-restricted interactions between CD8 and the α3 domain of class Iinfluence the magnitude of the xenogeneic response, J. Exp. Med.170:1091-1101; Vitiello et al. (1991), supra.

The transmembrane domain and cytoplasmic tail of mouse MHC class Iproteins also have important functions. One function of MHC Itransmembrane domain is to facilitate modulation by HLA-A2 of homotypiccell adhesion (to enhance or inhibit adhesion), presumably as the resultof cross-linking (or ligation) of surface MHC molecules. Wagner et al.(1994) Ligation of MHC Class I and Class II Molecules Can Lead toHeterologous Desensitization of Signal Transduction Pathways ThatRegulate Homotypic Adhesion in Human Lymphocytes, J. Immunol.152:5275-5287. Cell adhesion can be affected by mAbs that bind atdiverse epitopes of the HLA-A2 molecule, suggesting that there aremultiple sites on HLA-A2 implicated in modulating homotypic celladhesion; depending on the epitope bound, the affect can be to enhanceor to inhibit HLA-A2-dependent adhesion. Id.

The cytoplasmic tail, encoded by exons 6 and 7 of the MHC I gene, isreportedly necessary for proper expression on the cell surface and forLIR1-mediated inhibition of NK cell cytotoxicity. Gruda et al. (2007)Intracellular Cysteine Residues in the Tail of MHC Class I Proteins AreCrucial for Extracellular Recognition by Leukocyte Ig-Like Receptor 1,J. Immunol. 179:3655-3661. A cytoplasmic tail is required formultimerizaton of at least some MHC I molecules through formation ofdisulfide bonds on its cysteine residues, and thus may play a role inclustering and in recognition by NK cells. Lynch et al. (2009) Novel MHCClass I Structures on Exosomes, J. Immunol. 183:1884-1891.

The cytoplasmic domain of HLA-A2 contains a constitutivelyphosphorylated serine residue and a phosphorylatable tyrosine,although—in Jurkat cells—mutant HLA-A2 molecules lacking a cytoplasmicdomain appear normal with respect to expression, cytoskeletalassociation, aggregation, and endocytic internalization. Gur et al.(1997) Structural Analysis of Class I MHC Molecules: The CytoplasmicDomain Is Not Required for Cytoskeletal Association, Aggregation, andInternalization, Mol. Immunol. 34(2):125-132. Truncated HLA-A2 moleculeslacking the cytoplasmic domain are apparently normally expressed andassociate with β2 microglobulin. Id.

However, several studies have demonstrated that the cytoplasmic tail iscritical in intracellular trafficking, dendritic cell (DC)-mediatedantigen presentation, and CTL priming. A tyrosine residue encoded byexon 6 was shown to be required for MHC I trafficking through endosomalcompartments, presentation of exogenous antigens, and CTL priming; whiledeletion of exon 7 caused enhancement of anti-viral CTL responses. Lizeeet al. (2003) Control of Dendritic Cross-Presentation by the MajorHistocompatibility Complex Class I Cytoplasmic Domain, Nature Immunol.4:1065-73; Basha et al. (2008) MHC Class I Endosomal and LysosomalTrafficking Coincides with Exogenous Antigen Loading in Dendritic Cells,PLoS ONE 3: e3247; and Rodriguez-Cruz et al. (2011) Natural SpliceVariant of MHC Class I Cytoplasmic Tail Enhances Dendritic Cell-InducedCD8+T-Cell Responses and Boosts Anti-Tumor Immunity, PLoS ONE 6:e22939.

MHC class II complex comprises two non-covalently associated domains: anα chain and a β chain, also referred herein as an α polypeptide and a βpolypeptide (FIG. 1, right). The protein spans the plasma membrane; thusit contains an extracellular domain, a transmembrane domain, and acytoplasmic domain. The extracellular portion of the α chain includes α1and α2 domains, and the extracellular portion of the β chain includes β1and β2 domains. The α1 and β1 domains form a peptide-binding cleft onthe cell surface. Due to the three-dimensional conformation of thepeptide-binding cleft of the MHC II complex, there is theoretically noupper limit on the length of the bound antigen, but typically peptidespresented by MHC II are between 13 and 17 amino acids in length.

In addition to its interaction with the antigenic peptides, thepeptide-binding cleft of the MHC II molecule interacts with invariantchain (Ii) during the processes of MHC II complex formation and peptideacquisition. The α/β MHC II dimers assemble in the endoplasmic reticulumand associate with Ii chain, which is responsible for control of peptidebinding and targeting of the MHC II into endocytic pathway. In theendosome, Ii undergoes proteolysis, and a small fragment of Ii, ClassII-associated invariant chain peptide (CLIP), remains at thepeptide-binding cleft. In the endosome, under control of HLA-DM (inhumans), CLIP is exchanged for antigenic peptides.

MHC II interacts with T cell co-receptor CD4 at the hydrophobic creviceat the junction between α2 and β2 domains. Wang and Reinherz (2002)Structural Basis of T Cell Recognition of Peptides Bound to MHCMolecules, Molecular Immunology, 38:1039-49. When CD4 and T cellreceptor bind the same MHC II molecule complexed with a peptide, thesensitivity of a T cell to antigen is increased, and it requires100-fold less antigen for activation. See, Janeway's Immunobiology,7^(th) Ed., Murphy et al. eds., Garland Science, 2008, incorporatedherein by reference.

Numerous functions have been proposed for transmembrane and cytoplasmicdomains of MHC II. In the case of cytoplasmic domain, it has been shownto be important for intracellular signaling, trafficking to the plasmamembrane, and ultimately, antigen presentation. For example, it wasshown that T cell hybridomas respond poorly to antigen-presenting cells(APCs) transfected with MHC II β chains truncated at the cytoplasmicdomain, and induction of B cell differentiation is hampered. See, e.g.,Smiley et al. (1996) Truncation of the class II β-chain cytoplasmicdomain influences the level of class II/invariant chain-derived peptidecomplexes, Proc. Natl. Acad. Sci. USA, 93:241-44. Truncation of Class IImolecules seems to impair cAMP production. It has been postulated thatdeletion of the cytoplasmic tail of MHC II affects intracellulartrafficking, thus preventing the complex from coming across relevantantigens in the endocytic pathway. Smiley et al. (supra) demonstratedthat truncation of class II molecules at the cytoplasmic domain reducesthe number of CLIP/class II complexes, postulating that this affects theability of CLIP to effectively regulate antigen presentation.

It has been hypothesized that, since MHC II clustering is important forT cell receptor (TCR) triggering, if MHC II molecules truncated at thecytoplasmic domain were prevented from binding cytoskeleton and thusaggregating, antigen presentation to T cells would be affected.Ostrand-Rosenberg et al. (1991) Abrogation of Tumorigenicity by MHCClass II Antigen Expression Requires the Cytoplasmic Domain of the ClassII Molecule, J. Immunol. 147:2419-22. In fact, it was recently shownthat HLA-DR truncated at the cytoplasmic domain failed to associate withthe cytoskeleton following oligomerization. El Fakhy et al. (2004)Delineation of the HLA-DR Region and the Residues Involved in theAssociation with the Cytoskeleton, J. Biol. Chem. 279:18472-80.Importantly, actin cytoskeleton is a site of localized signaltransduction activity, which can effect antigen presentation. Inaddition to association with cytoskeleton, recent studies have alsoshown that up to 20% of all HLA-DR molecules constitutively reside inthe lipid rafts of APCs, which are microdomains rich in cholesterol andglycosphingolipids, and that such localization is important for antigenpresentation, immune synapse formation, and MHC II-mediated signaling.See, e.g., Dolan et al. (2004) Invariant Chain and the MHC IICytoplasmic Domains Regulate Localization of MHC Class II Molecules toLipid Rafts in Tumor Cell-Based Vaccines, J. Immunol. 172:907-14. Dolanet al. suggested that truncation of cytoplasmic domain of MHC II reducesconstitutive localization of MHC II to lipid rafts.

In addition, the cytoplasmic domain of MHC II, in particular the βchain, contains a leucine residue that is subject to ubiquitination byubiquitin ligase, membrane-associated RING-CH I (MARCH I), whichcontrols endocytic trafficking, internalization, and degradation of MHCII; and it has been shown that MARCH-mediated ubiquitination ceases upondendritic cell maturation resulting in increased levels of MHC II at theplasma membrane. Shin et al. (2006) Surface expression of MHC class IIin dendritic cells is controlled by regulated ubiquitination, Nature444:115-18; De Gassart et al. (2008) MHC class II stabilization at thesurface of human dendritic cells is the result of maturation-dependentMARCH I down-regulation, Proc. Natl. Acad. Sci. USA 105:3491-96.

Transmembrane domains of α and β chains of MHC II interact with eachother and this interaction is important for proper assembly of class IIMHC complex. Cosson and Bonifacino (1992) Role of Transmembrane DomainInteractions in the Assembly of Class II MHC Molecules, Nature258:659-62. In fact, MHC II molecules in which the transmembrane domainsof the α and β chains were replaced by the α chain of IL-2 receptor wereretained in the ER and were barely detectable at the cell surface. Id.Through mutagenesis studies, conserved Gly residues at the α and βtransmembrane domains were found to be responsible for MHC II assemblyat the cell surface. Id. Thus, both transmembrane and cytoplasmicdomains are crucial for the proper function of the MHC II complex.

In various embodiments, provided herein is a genetically modifiednon-human animal, e.g., rodent (e.g., mouse or rat) comprising in itsgenome a nucleotide sequence encoding a human or humanized MHC Ipolypeptide and a nucleotide sequence encoding human or humanized MHC IIprotein. The MHC I nucleotide sequence may encode an MHC I polypeptidethat is partially human and partially non-human, e.g., chimerichuman/non-human MHC I polypeptide, and the MHC II nucleotide sequencemay encode an MHC II protein that is partially human and partiallynon-human, e.g., chimeric human/non-human MHC II protein (e.g.,comprising chimeric human/non-human MHC II α and β polypeptides). Insome aspects, the animal does not express endogenous MHC I and IIpolypeptides, e.g., functional endogenous MHC I and II polypeptides. Insome embodiments, the only MHC I and MHC II molecules expressed on acell surface of the animal are chimeric MHC I and II molecules.

A genetically modified non-human animal comprising in its genome, e.g.,at the endogenous locus, a nucleotide sequence encoding a chimerichuman/non-human MHC I polypeptide is disclosed in U.S. PatentApplication Publication Nos. 20130111617 and 20130185819, whichapplications are incorporated herein by reference in their entireties. Agenetically modified non-human animal comprising in its genome, e.g., atthe endogenous locus, a nucleotide sequence encoding humanized, e.g.,chimeric human/non-human MHC II polypeptides is disclosed in U.S. Pat.Nos. 8,847,005 and 9,043,996, which applications are incorporated hereinby reference in their entireties. A genetically modified non-humananimal comprising in its genome, e.g., at the endogenous locus, anucleotide sequence encoding a chimeric human/non-human MHC Ipolypeptide and comprising in its genome, e.g., at the endogenous locus,a nucleotide sequence encoding humanized, e.g., chimeric human/non-humanMHC II polypeptides, is disclosed in U.S. Patent Application PublicationNo. 20140245467, which application is incorporated herein by referencein its entirety.

In various embodiments provided herein is a genetically modifiednon-human animal comprising in its genome, e.g., at endogenous MHClocus, a first nucleotide sequence encoding a chimeric human/non-humanMHC I polypeptide, wherein a human portion of the chimeric MHC Ipolypeptide comprises an extracellular domain of a human MHC Ipolypeptide; a second nucleotide sequence encoding a chimerichuman/non-human MHC II α polypeptide, wherein a human portion of thechimeric MHC II α polypeptide comprises an extracellular domain of ahuman MHC II α polypeptide; and a third nucleotide sequence encoding achimeric human/non-human MHC II β polypeptide, wherein a human portionof the chimeric MHC II β polypeptide comprises an extracellular domainof a human MHC II β polypeptide; wherein the non-human animal expressesfunctional chimeric human/non-human MHC I and MHC II proteins from itsendogenous non-human MHC locus. In one embodiment, the first, second,and/or third nucleotide sequences are located the endogenous non-humanMHC locus. In one embodiment, wherein the non-human animal is a mouse,the first, second, and/or third nucleotide sequences are located at theendogenous mouse MHC locus on mouse chromosome 17. In one embodiment,the first nucleotide sequence is located at the endogenous non-human MHCI locus. In one embodiment, the second nucleotide sequence is located atthe endogenous non-human MHC II α locus. In one embodiment, the thirdnucleotide sequence is located at the endogenous non-human MHC II βlocus.

In one embodiment, the non-human animal only expresses the chimerichuman/non-human MHC I, MHC II α and/or MHC β II polypeptides and doesnot express endogenous non-human MHC polypeptides (e.g., functionalendogenous MHC I, II α and/or II β polypeptides) from the endogenousnon-human MHC locus. In one embodiment, the animal described hereinexpresses a functional chimeric MHC I and a functional chimeric MHC IIon the surface of its cells, e.g., antigen presenting cells, etc. In oneembodiment, the only MHC I and MHC II expressed by the animal on a cellsurface are chimeric MHC I and chimeric MHC II, and the animal does notexpress any endogenous MHC I and MHC II on a cell surface.

In one embodiment, the chimeric human/non-human MHC I polypeptidecomprises in its human portion a peptide binding domain of a human MHC Ipolypeptide. In one aspect, the human portion of the chimericpolypeptide comprises an extracellular domain of a human MHC I. In thisembodiment, the human portion of the chimeric polypeptide comprises anextracellular domain of an α chain of a human MHC I. In one embodiment,the human portion of the chimeric polypeptide comprises α1 and α2domains of a human MHC I. In another embodiment, the human portion ofthe chimeric polypeptide comprises α1, α2, and α3 domains of a human MHCI.

In one aspect, a human portion of the chimeric MHC II α polypeptideand/or a human portion of the chimeric MHC II β polypeptide comprises apeptide-binding domain of a human MHC II α polypeptide and/or human MHCII β polypeptide, respectively. In one aspect, a human portion of thechimeric MHC II α and/or β polypeptide comprises an extracellular domainof a human MHC II α and/or β polypeptide, respectively. In oneembodiment, a human portion of the chimeric MHC II α polypeptidecomprises α1 domain of a human MHC II α polypeptide; in anotherembodiment, a human portion of the chimeric MHC II α polypeptidecomprises α1 and α2 domains of a human MHC II α polypeptide. In anadditional embodiment, a human portion of the chimeric MHC II βpolypeptide comprises β1 domain of a human MHC II β polypeptide; inanother embodiment, a human portion of the chimeric MHC II β polypeptidecomprises β1 and β2 domains of a human MHC II β polypeptide.

In some embodiments, the human or humanized MHC I polypeptide may bederived from a functional human HLA molecule encoded by any of HLA-A,HLA-B, HLA-C, HLA-E, HLA-F, or HLA-G loci. The human or humanized MHC IIpolypeptide may be derived from a functional human HLA molecule encodedby an of HLA-DP, -DQ, and -DR loci. A list of commonly used HLA antigensand alleles is described in Shankarkumar et al. ((2004) The HumanLeukocyte Antigen (HLA) System, Int. J. Hum. Genet. 4(2):91-103),incorporated herein by reference. Shankarkumar et al. also present abrief explanation of HLA nomenclature used in the art. Additionalinformation regarding HLA nomenclature and various HLA alleles can befound in Holdsworth et al. (2009) The HLA dictionary 2008: a summary ofHLA-A, -B, -C, -DRB1/3/4/5, and DQB1 alleles and their association withserologically defined HLA-A, -B, -C, -DR, and -DQ antigens, TissueAntigens 73:95-170, and a recent update by Marsh et al. (2010)Nomenclature for factors of the HLA system, 2010, Tissue Antigens75:291-455, both incorporated herein by reference. In some embodiments,the MHC I or MHC II polypeptides may be derived from any functionalhuman HLA-A, B, C, DR, or DQ molecules. Thus, the human or humanized MHCI and/or II polypeptides may be derived from any functional human HLAmolecules described therein. In some embodiments, all MHC I and MHC IIpolypeptides expressed on a cell surface comprise a portion derived fromhuman HLA molecules.

Of particular interest are human HLA molecules, specific polymorphic HLAalleles, known to be associated with a number of human diseases, e.g.,human autoimmune diseases. In fact, specific polymorphisms in HLA locihave been identified that correlate with development of rheumatoidarthritis, type I diabetes, Hashimoto's thyroiditis, multiple sclerosis,myasthenia gravis, Graves' disease, systemic lupus erythematosus, celiacdisease, Crohn's disease, ulcerative colitis, and other autoimmunedisorders. See, e.g., Wong and Wen (2004) What can the HLA transgenicmouse tell us about autoimmune diabetes?, Diabetologia 47:1476-87;Taneja and David (1998) HLA Transgenic Mice as Humanized Mouse Models ofDisease and Immunity, J. Clin. Invest. 101:921-26; Bakker et al. (2006),A high-resolution HLA and SNP haplotype map for disease associationstudies in the extended human MHC, Nature Genetics 38:1166-72 andSupplementary Information; and International MHC and AutoimmunityGenetics Network (2009) Mapping of multiple susceptibility variantswithin the MHC region for 7 immune-mediated diseases, Proc. Natl. Acad.Sci. USA 106:18680-85. Thus, the human or humanized MHC I and/or IIpolypeptides may be derived from a human HLA molecule known to beassociated with a particular disease, e.g., autoimmune disease.

In one specific aspect, the human or humanized MHC I polypeptide isderived from human HLA-A. In a specific embodiment, the HLA-Apolypeptide is an HLA-A2 polypeptide (e.g., and HLA-A2.1 polypeptide).In one embodiment, the HLA-A polypeptide is a polypeptide encoded by anHLA-A*0201 allele, e.g., HLA-A*02:01:01:01 allele. The HLA-A*0201 alleleis commonly used amongst the North American population. Although thepresent Examples describe this particular HLA sequence, any suitableHLA-A sequence is encompassed herein, e.g., polymorphic variants ofHLA-A2 exhibited in human population, sequences with one or moreconservative or non-conservative amino acid modifications, nucleic acidsequences differing from the sequence described herein due to thedegeneracy of genetic code, etc.

In another specific aspect, the human portion of the chimeric MHC Ipolypeptide is derived from human MHC I selected from HLA-B and HLA-C.In one aspect, it is derived from HLA-B, e.g., HLA-B27. In anotheraspect, it is derived from HLA-A3, -B7, -Cw6, etc.

In one specific aspect, the human portions of the humanized MHC II α andβ polypeptides described herein are derived from human HLA-DR, e.g.,HLA-DR2. Typically, HLA-DR α chains are monomorphic, e.g., the α chainof HLA-DR complex is encoded by HLA-DRA gene (e.g., HLA-DRα*01 gene). Onthe other hand, the HLA-DR β chain is polymorphic. Thus, HLA-DR2comprises an a chain encoded by HLA-DRA gene and a β chain encoded byHLA-DR1β*1501 gene. Although the present Examples describe theseparticular HLA sequences, any suitable HLA-DR sequences are encompassedherein, e.g., polymorphic variants exhibited in human population,sequences with one or more conservative or non-conservative amino acidmodifications, nucleic acid sequences differing from the sequencesdescribed herein due to the degeneracy of genetic code, etc.

The human portions of the chimeric MHC II α and/or β polypeptide may beencoded by nucleotide sequences of HLA alleles known to be associatedwith common human diseases. Such HLA alleles include, but are notlimited to, HLA-DRB1*0401, -DRB1*0301, -DQA1*0501, -DQB1*0201,-DRB1*1501, -DRB1*1502, -DQB1*0602, -DQA1*0102, -DQA1*0201, -DQB1*0202,-DQA1*0501, and combinations thereof. For a summary of HLAallele/disease associations, see Bakker et al. (2006), supra,incorporated herein by reference.

In one aspect, the non-human portion of a chimeric human/non-human MHCI, MHC II α and/or MHC II β polypeptide(s) comprises transmembraneand/or cytoplasmic domains of an endogenous non-human (e.g., rodent,e.g., mouse, rat, etc.) MHC I, MHC II α and/or MHC II β polypeptide(s),respectively. Thus, the non-human portion of the chimerichuman/non-human MHC I polypeptide may comprise transmembrane and/orcytoplasmic domains of an endogenous non-human MHC I polypeptide. Thenon-human portion of a chimeric MHC II α polypeptide may comprisetransmembrane and/or cytoplasmic domains of an endogenous non-human MHCII α polypeptide. The non-human portion of a chimeric human/non-humanMHC II β polypeptide may comprise transmembrane and/or cytoplasmicdomains of an endogenous non-human MHC II β polypeptide. In one aspect,the non-human animal is mouse, and a non-human portion of the chimericMHC I polypeptide is derived from a mouse H-2K protein. In one aspect,the animal is a mouse, and non-human portions of the chimeric MHC II αand β polypeptides are derived from a mouse H-2E protein. Thus, anon-human portion of the chimeric MHC I polypeptide may comprisetransmembrane and cytoplasmic domains derived from a mouse H-2K, andnon-human portions of the chimeric MHC II α and β polypeptides maycomprise transmembrane and cytoplasmic domains derived from a mouse H-2Eprotein. Although specific H-2K and H-2E sequences are contemplated inthe Examples, any suitable sequences, e.g., polymorphic variants,conservative/non-conservative amino acid substitutions, etc., areencompassed herein. In one aspect, the non-human animal is a mouse, andthe mouse does not express functional endogenous MHC polypeptides fromits H-2D locus. In some embodiments, the mouse is engineered to lack allor a portion of an endogenous H-2D locus. In other aspects, the mousedoes not express any functional endogenous mouse MHC I and MHC II on acell surface.

A chimeric human/non-human polypeptide may be such that it comprises ahuman or a non-human leader (signal) sequence. In one embodiment, thechimeric MHC I polypeptide comprises a non-human leader sequence of anendogenous MHC I polypeptide. In one embodiment, the chimeric MHC II αpolypeptide comprises a non-human leader sequence of an endogenous MHCII α polypeptide. In one embodiment, the chimeric MHC II β polypeptidecomprises a non-human leader sequence of an endogenous MHC II βpolypeptide. In an alternative embodiment, the chimeric MHC I, MHC II αand/or MHC II β polypeptide(s) comprises a non-human leader sequence ofMHC I, MHC II α and/or MHC II β polypeptide(s), respectively, fromanother non-human animal, e.g., another rodent or another mouse strain.Thus, the nucleotide sequence encoding the chimeric MHC I, MHC II αand/or MHC II β polypeptide may be operably linked to a nucleotidesequence encoding a non-human MHC I, MHC II α and/or MHC II β leadersequence, respectively. In yet another embodiment, the chimeric MHC I,MHC II α and/or MHC II β polypeptide(s) comprises a human leadersequence of human MHC I, human MHC II α and/or human MHC II βpolypeptide, respectively (e.g., a leader sequence of human HLA-A2,human HLA-DRA and/or human HLA-DRβ1*1501, respectively).

A chimeric human/non-human MHC I, MHC II α and/or MHC II β polypeptidemay comprise in its human portion a complete or substantially completeextracellular domain of a human MHC I, human MHC II α and/or human MHCII β polypeptide, respectively. Thus, a human portion may comprise atleast 80%, preferably at least 85%, more preferably at least 90%, e.g.,95% or more of the amino acids encoding an extracellular domain of ahuman MHC I, human MHC II α and/or human MHC II β polypeptide (e.g.,human HLA-A2, human HLA-DRA and/or human HLA-DRβ1*1501). In one example,substantially complete extracellular domain of the human MHC I, humanMHC II α and/or human MHC II β polypeptide lacks a human leadersequence. In another example, the chimeric human/non-human MHC I,chimeric human/non-human MHC II α and/or the chimeric human/non-humanMHC II β polypeptide comprises a human leader sequence.

Moreover, the chimeric MHC I, MHC II α and/or MHC II β polypeptide maybe operably linked to (e.g., be expressed under the regulatory controlof) endogenous non-human promoter and regulatory elements, e.g., mouseMHC I, MHC II α and/or MHC II β regulatory elements, respectively. Sucharrangement will facilitate proper expression of the chimeric MHC Iand/or MHC II polypeptides in the non-human animal, e.g., during immuneresponse in the non-human animal.

The genetically modified non-human animal may be selected from a groupconsisting of a mouse, rat, rabbit, pig, bovine (e.g., cow, bull,buffalo), deer, sheep, goat, chicken, cat, dog, ferret, primate (e.g.,marmoset, rhesus monkey). For the non-human animals where suitablegenetically modifiable ES cells are not readily available, other methodsare employed to make a non-human animal comprising the geneticmodification. Such methods include, e.g., modifying a non-ES cell genome(e.g., a fibroblast or an induced pluripotent cell) and employingnuclear transfer to transfer the modified genome to a suitable cell,e.g., an oocyte, and gestating the modified cell (e.g., the modifiedoocyte) in a non-human animal under suitable conditions to form anembryo.

In one aspect, the non-human animal is a mammal. In one aspect, thenon-human animal is a small mammal, e.g., of the superfamily Dipodoideaor Muroidea. In one embodiment, the genetically modified animal is arodent. In one embodiment, the rodent is selected from a mouse, a rat,and a hamster. In one embodiment, the rodent is selected from thesuperfamily Muroidea. In one embodiment, the genetically modified animalis from a family selected from Calomyscidae (e.g., mouse-like hamsters),Cricetidae (e.g., hamster, New World rats and mice, voles), Muridae(true mice and rats, gerbils, spiny mice, crested rats), Nesomyidae(climbing mice, rock mice, white-tailed rats, Malagasy rats and mice),Platacanthomyidae (e.g., spiny dormice), and Spalacidae (e.g., molerates, bamboo rats, and zokors). In a specific embodiment, thegenetically modified rodent is selected from a true mouse or rat (familyMuridae), a gerbil, a spiny mouse, and a crested rat. In one embodiment,the genetically modified mouse is from a member of the family Muridae.In one embodiment, the animal is a rodent. In a specific embodiment, therodent is selected from a mouse and a rat. In one embodiment, thenon-human animal is a mouse.

In one embodiment, the non-human animal is a rodent that is a mouse of aC57BL strain selected from C57BL/A, C57BL/An, C57BL/GrFa, C57BL/KaLwN,C57BL/6, C57BL/6J, C57BL/6ByJ, C57BL/6NJ, C57BL/10, C57BL/10ScSn,C57BL/10Cr, and C57BL/Ola. In another embodiment, the mouse is a 129strain selected from the group consisting of a strain that is 129P1,129P2, 129P3, 129X1, 129S1 (e.g., 129S1/SV, 12951/Svlm), 129S2, 129S4,129S5, 129S9/SvEvH, 129S6 (129/SvEvTac), 129S7, 129S8, 129T1, 129T2(see, e.g., Festing et al. (1999) Revised nomenclature for strain 129mice, Mammalian Genome 10:836, see also, Auerbach et al (2000)Establishment and Chimera Analysis of 129/SvEv- and C57BL/6-DerivedMouse Embryonic Stem Cell Lines). In one embodiment, the geneticallymodified mouse is a mix of an aforementioned 129 strain and anaforementioned C57BL/6 strain. In another embodiment, the mouse is a mixof aforementioned 129 strains, or a mix of aforementioned BL/6 strains.In one embodiment, the 129 strain of the mix is a 129S6 (129/SvEvTac)strain. In another embodiment, the mouse is a BALB strain, e.g., BALB/cstrain. In yet another embodiment, the mouse is a mix of a BALB strainand another aforementioned strain. In some embodiments, the mouse strainis such that a genetically wild-type mouse of that strain only expressesMHC I polypeptides derived from H-2K and H-2D on a cell surface andlacks endogenous H-2L gene.

In one embodiment, the non-human animal is a rat. In one embodiment, therat is selected from a Wistar rat, an LEA strain, a Sprague Dawleystrain, a Fischer strain, F344, F6, and Dark Agouti. In one embodiment,the rat strain is a mix of two or more strains selected from the groupconsisting of Wistar, LEA, Sprague Dawley, Fischer, F344, F6, and DarkAgouti.

Thus, in one embodiment, the invention relates to a genetically modifiedmouse that comprises in its genome a first nucleotide sequence encodinga chimeric human/mouse MHC I, a second nucleotide sequence encoding achimeric human/mouse MHC II α, and a third nucleotide sequence encodinga chimeric human/mouse MHC II β polypeptides. A human portion of thechimeric MHC I, MHC II α, and MHC II β may comprise an extracellulardomain of a human MHC I, MHC II α, and MHC II β, respectively. In oneembodiment, the mouse expresses functional chimeric human/mouse MHC I,MHC II α, and MHC II β polypeptides from its endogenous mouse MHC locus.In one embodiment, the mouse does not express functional mouse MHCpolypeptides, e.g., functional mouse MHC I, MHC II α, and MHC II βpolypeptides, from its endogenous mouse MHC locus. In one embodiment,the mouse does not express functional endogenous MHC polypeptides fromits H-2D locus. In some embodiments, the mouse is engineered to lack allor a portion of an endogenous H-2D locus. In other embodiments, the onlyMHC I and MHC II expressed by the mouse on a cell surface are chimericMHC I and II.

In one embodiment, a human portion of the chimeric human/mouse MHC Ipolypeptide comprises a peptide binding domain or an extracellulardomain of a human MHC I (e.g., human HLA-A, e.g., human HLA-A2, e.g.,human HLA-A2.1). In some embodiments, the mouse does not express apeptide binding or an extracellular domain of an endogenous mouse MHC Ipolypeptide from its endogenous mouse MHC I locus. The peptide bindingdomain of the chimeric human/mouse MHC I may comprise human α1 and α2domains. Alternatively, the peptide binding domain of the chimerichuman/mouse MHC I may comprise human α1, α2, and α3 domains. In oneaspect, the extracellular domain of the chimeric human/mouse MHC Icomprises an extracellular domain of a human MHC I α chain. In oneembodiment, the endogenous mouse MHC I locus is an H-2K (e.g., H-2Kb)locus, and the mouse portion of the chimeric MHC I polypeptide comprisestransmembrane and cytoplasmic domains of a mouse H-2K (e.g., H-2Kb)polypeptide. Thus, in one embodiment, the mouse of the inventioncomprises at its endogenous mouse MHC I locus a nucleotide sequenceencoding a chimeric human/mouse MHC I, wherein a human portion of thechimeric polypeptide comprises an extracellular domain of a human HLA-A2(e.g., HLA-A2.1) polypeptide and a mouse portion comprises transmembraneand cytoplasmic domains of a mouse H-2K (e.g., H-2Kb) polypeptide, and amouse expresses a chimeric human/mouse HLA-A2/H-2K protein. In otherembodiment, the mouse portion of the chimeric MHC I polypeptide may bederived from other mouse MHC I, e.g., H-2D, H-2L, etc.; and the humanportion of the chimeric MHC I polypeptide may be derived from otherhuman MHC I, e.g., HLA-B, HLA-C, etc. In one aspect, the mouse does notexpress a functional endogenous H-2K polypeptide from its endogenousmouse H-2K locus. In one embodiment, the mouse does not expressfunctional endogenous MHC polypeptides from its H-2D locus. In someembodiments, the mouse is engineered to lack all or a portion of anendogenous H-2D locus. In other embodiments, the only MHC I polypeptidesexpressed by the mouse on a cell surface are chimeric human/mouse MHC Ipolypeptides.

In one embodiment, a human portion of the chimeric human/mouse MHC II αpolypeptide comprises a human MHC II α peptide binding or extracellulardomain and a human portion of the chimeric human/mouse MHC II βpolypeptide comprises a human MHC II β peptide binding or extracellulardomain. In some embodiments, the mouse does not express a peptidebinding or an extracellular domain of endogenous mouse α and/or βpolypeptide from an endogenous mouse locus (e.g., H-2A and/or H-2Elocus). In some embodiments, the mouse comprises a genome that lacks agene that encodes a functional MHC class II molecule comprising anH-2Ab1, H-2Aa, H-2Eb1, H-2Eb2, H-2Ea, and a combination thereof. In someembodiments, the only MHC II polypeptides expressed by the mouse on acell surface are chimeric human/mouse MHC II polypeptides. Thepeptide-binding domain of the chimeric human/mouse MHC II α polypeptidemay comprise human α1 domain and the peptide-binding domain of thechimeric human/mouse MHC II β polypeptide may comprise a human β1domain; thus, the peptide-binding domain of the chimeric MHC II complexmay comprise human α1 and β1 domains. The extracellular domain of thechimeric human/mouse MHC II α polypeptide may comprise human α1 and α2domains and the extracellular domain of the chimeric human/mouse MHC IIβ polypeptide may comprise human β1 and β2 domains; thus, theextracellular domain of the chimeric MHC II complex may comprise humanα1, α2, β1 and β2 domains. In one embodiment, the mouse portion of thechimeric MHC II complex comprises transmembrane and cytosolic domains ofmouse MHC II, e.g. mouse H-2E (e.g., transmembrane and cytosolic domainsof mouse H-2E α and β chains). Thus, in one embodiment, the mouse of theinvention comprises at its endogenous mouse MHC II locus a nucleotidesequence encoding a chimeric human/mouse MHC II α, wherein a humanportion of the chimeric MHC II α polypeptide comprises an extracellulardomain derived from an α chain of a human MHC II (e.g., α chain ofHLA-DR2) and a mouse portion comprises transmembrane and cytoplasmicdomains derived from an α chain of a mouse MHC II (e.g., H-2E); and amouse comprises at its endogenous mouse MHC II locus a nucleotidesequence encoding a chimeric human/mouse MHC II β, wherein a humanportion of the chimeric MHC II β polypeptide comprises an extracellulardomain derived from a β chain of a human MHC II (e.g., β chain ofHLA-DR2) and a mouse portion comprises transmembrane and cytoplasmicdomains derived from a β chain of a mouse MHC II (e.g., H-2E); whereinthe mouse expresses a chimeric human/mouse HLA-DR2/H-2E protein. Inother embodiment, the mouse portion of the chimeric MHC II protein maybe derived from other mouse MHC II, e.g., H-2A, etc.; and the humanportion of the chimeric MHC II protein may be derived from other humanMHC II, e.g., HLA-DQ, etc. In one aspect, the mouse does not expressfunctional endogenous H-2A and H-2E polypeptides from their endogenousmouse loci (e.g., the mouse does not express H-2Ab1, H-2Aa, H-2Eb1,H-2Eb2, and H-2Ea polypeptides). In one aspect, the mouse does notexpress functional endogenous MHC polypeptides from its H-2D locus. Insome embodiments, the mouse is engineered to lack all or a portion of anendogenous H-2D locus. In some embodiments, the mouse lacks expressionof any endogenous MHC I or MHC II molecule on a cell surface.

In a further embodiment, a non-human animal of the invention, e.g., arodent, e.g., a mouse, comprises at an endogenous β2 microglobulin locusa nucleotide sequence encoding a human or humanized β2 microglobulin. β2microglobulin or the light chain of the MHC class I complex (alsoabbreviated “β2M”) is a small (12 kDa) non-glycosylated protein, thatfunctions primarily to stabilize the MHC I α chain. Generation of humanor humanized microglobulin animals is described in detail in U.S. PatentPublication No. 20130111617, and is incorporated herein by reference. Amouse comprising a humanized MHC locus as described in the presentdisclosure, and a human or humanized β2 microglobulin locus as describedin U.S. Patent Publication No. 2013011, may be generated by any methodsknown in the art, e.g., breeding, or alternatively, using homologousrecombination in ES cells.

Various other embodiments of a genetically modified non-human animal,e.g. rodent, e.g., rat or mouse, would be evident to one skilled in theart from the present disclosure and from the disclosure of U.S. PatentPublication No. 20130111617 and U.S. Pat. No. 8,847,005 incorporatedherein by reference.

In various aspects of the invention, the sequence(s) encoding a chimerichuman/non-human MHC I and MHC II polypeptides are located at anendogenous non-human MHC locus (e.g., mouse H-2K and/or H-2E locus). Inone embodiment, this results in a replacement of an endogenous MHCgene(s) or a portion thereof with a nucleotide sequence(s) encoding ahuman or humanized MHC I or MHC II polypeptides. Since the nucleotidesequences encoding MHC I, MHC II α and MHC II β polypeptides are locatedin proximity to one another on the chromosome, in order to achieve thegreatest success in humanization of both MHC I and MHC II in one animal,the MHC I and MHC II loci should be targeted sequentially. Thus, alsoprovided herein are methods of generating a genetically modifiednon-human animal comprising nucleotide sequences encoding chimerichuman/non-human MHC I, MHC II α and MHC II β polypeptides as describedherein.

In some embodiments, the method utilizes a targeting construct madeusing VELOCIGENE® technology, introducing the construct into ES cells,and introducing targeted ES cell clones into a mouse embryo usingVELOCIMOUSE® technology, as described in the Examples.

The nucleotide constructs used for generating non-human animalsdescribed herein are also provided. In one aspect, the nucleotideconstruct comprises: 5′ and 3′ non-human homology arms, a human DNAfragment comprising human MHC gene sequences (e.g., human HLA-A2 orhuman HLA-DR4 gene sequences), and a selection cassette flanked byrecombination sites. In one embodiment, the human DNA fragment is agenomic fragment that comprises both introns and exons of a human MHCgene (e.g., human HLA-A2 or HLA-DR2 gene). In one embodiment, thenon-human homology arms are homologous to a non-human MHC locus (e.g.,MHC I or MHC II locus).

A selection cassette is a nucleotide sequence inserted into a targetingconstruct to facilitate selection of cells (e.g., ES cells) that haveintegrated the construct of interest. A number of suitable selectioncassettes are known in the art. Commonly, a selection cassette enablespositive selection in the presence of a particular antibiotic (e.g.,Neo, Hyg, Pur, CM, Spec, etc.). In addition, a selection cassette may beflanked by recombination sites, which allow deletion of the selectioncassette upon treatment with recombinase enzymes. Commonly usedrecombination sites are loxP* and Frt, recognized by Cre and Flpenzymes, respectively, but others are known in the art. In oneembodiment, the selection cassette is located at the 5′ end the humanDNA fragment. In another embodiment, the selection cassette is locatedat the 3′ end of the human DNA fragment. In another embodiment, theselection cassette is located within the human DNA fragment. In anotherembodiment, the selection cassette is located within an intron of thehuman DNA fragment.

In one embodiment, the 5′ and 3′ non-human homology arms comprisegenomic sequence at 5′ and 3′ locations, respectively, of an endogenousnon-human (e.g., murine) MHC class I or class II gene locus (e.g., 5′ ofthe first leader sequence and 3′ of the α3 exon of the mouse MHC I gene,or upstream of mouse H-2Ab1 gene and downstream of mouse H-2Ea gene). Inone embodiment, the endogenous MHC class I locus is selected from mouseH-2K, H-2D and H-2L. In a specific embodiment, the endogenous MHC classI locus is mouse H-2K. In one embodiment, the endogenous MHC II locus isselected from mouse H-2E and H-2A. In one embodiment, the engineered MHCII construct allows replacement of both mouse H-2E and H-2A genes. Inone embodiment, the mouse does not express functional endogenous MHCpolypeptides from its H-2D locus. In some embodiments, the mouse isengineered to lack all or a portion of an endogenous H-2D locus. Inanother embodiment, the mouse does not express any functional endogenousMHC I and MHC II polypeptides on a cell surface. In one embodiment, theonly MHC I and MHC II expressed by the mouse on a cell surface arechimeric human/mouse MHC I and MHC II.

Thus, in one embodiment, provided herein is a method of generating agenetically engineered non-human animal (e.g., rodent, e.g., rat ormouse) capable of expressing humanized MHC I and II proteins comprisingreplacing at an endogenous non-human MHC II locus a nucleotide sequenceencoding a non-human MHC II complex with a nucleotide sequence encodinga chimeric human/non-human MHC II complex to generate a first non-humananimal; and replacing at an endogenous non-human MHC I locus anucleotide sequence encoding a non-human MHC I polypeptide with anucleotide sequence encoding a chimeric human/non-human MHC Ipolypeptide to generate a second non-human animal. In one embodiment,the steps of replacing nucleotide sequences comprise homologousrecombination in ES cells. In one embodiment, the second non-humananimal is generated by homologous recombination in ES cells bearingnucleotide sequences encoding chimeric human/non-human MHC II complex.In one embodiment, the non-human animal is a mouse, and the first orsecond mouse does not express functional endogenous MHC polypeptidesfrom its H-2D locus. In some embodiments, the first or second mouse isengineered to lack all or a portion of an endogenous H-2D locus.Alternatively, also provided herein is a method of generating agenetically engineered non-human animal (e.g., rodent, e.g., rat ormouse) capable of expressing humanized MHC I and II proteins comprisingreplacing at an endogenous non-human MHC I locus a nucleotide sequenceencoding a non-human MHC I polypeptide with a nucleotide sequenceencoding a chimeric human/non-human MHC I polypeptide to generate afirst non-human animal; and replacing at an endogenous non-human MHC IIlocus a nucleotide sequence encoding a non-human MHC II complex with anucleotide sequence encoding a chimeric human/non-human MHC II complexto generate a second non-human animal. In such embodiment, the secondnon-human animal is generated by homologous recombination in ES cellsbearing a nucleotide sequence encoding chimeric human/non-human MHC Ipolypeptide.

Upon completion of gene targeting, ES cells or genetically modifiednon-human animals are screened to confirm successful incorporation ofexogenous nucleotide sequence of interest or expression of exogenouspolypeptide. Numerous techniques are known to those skilled in the art,and include (but are not limited to) Southern blotting, long PCR,quantitative PCT (e.g., real-time PCR using TAQMAN®), fluorescence insitu hybridization, Northern blotting, flow cytometry, Western analysis,immunocytochemistry, immunohistochemistry, etc. In one example,non-human animals (e.g., mice) bearing the genetic modification ofinterest can be identified by screening for loss of mouse allele and/orgain of human allele using a modification of allele assay described inValenzuela et al. (2003) High-throughput engineering of the mouse genomecoupled with high-resolution expression analysis, Nature Biotech.21(6):652-659. Other assays that identify a specific nucleotide or aminoacid sequence in the genetically modified animals are known to thoseskilled in the art.

In one aspect, a cell that expresses a chimeric human/non-human MHC Iand MHC II proteins (e.g., HLA-A2/H-2K and HLA-DR2/H-2E proteins) isprovided. In one aspect, the cell is a mouse cell that does not expressfunctional endogenous MHC polypeptides from its H-2D locus. In someembodiments, the cell is a mouse cell is engineered to lack all or aportion of an endogenous H-2D locus. In some embodiments, the cell is amouse cell that does not express any endogenous MHC I and MHC IIpolypeptide on its surface. In one embodiment, the cell comprises anexpression vector comprising a chimeric MHC class I sequence andchimeric MHC class II sequence as described herein. In one embodiment,the cell is selected from CHO, COS, 293, HeLa, and a retinal cellexpressing a viral nucleic acid sequence (e.g., a PERC.6™ cell).

A chimeric MHC II complex comprising an extracellular domain of HLA-DR2described herein may be detected by anti-HLA-DR antibodies. Thus, a celldisplaying chimeric human/non-human MHC II polypeptide may be detectedand/or selected using anti-HLA-DR antibody. The chimeric MHC I complexcomprising an extracellular domain of HLA-A2 described herein may bedetected using anti-HLA-A, e.g., anti-HLA-A2 antibodies. Thus, a celldisplaying a chimeric human/non-human MHC I polypeptide may be detectedand/or selected using anti-HLA-A antibody. Antibodies that recognizeother HLA alleles are commercially available or can be generated, andmay be used for detection/selection.

Although the Examples that follow describe a genetically engineeredanimal whose genome comprises a replacement of a nucleotide sequenceencoding mouse H-2K, and H-2A and H-2E proteins with a nucleotidesequence encoding a chimeric human/mouse HLA-A2/H-2K and HLA-DR2/H-2Eprotein, respectively, one skilled in the art would understand that asimilar strategy may be used to introduce chimeras comprising otherhuman MHC I and II genes (other HLA-A, HLA-B, and HLA-C; and otherHLA-DR, HLA-DP and HLA-DQ genes). Such animals comprising multiplechimeric human/non-human (e.g., human/rodent, e.g., human/mouse) MHC Iand MHC II genes at endogenous MHC loci are also provided.

In various embodiments of the invention, the mouse that compriseschimeric human/mouse MHC I and MHC II loci and expresses only chimerichuman/mouse MHC I and MHC II on a cell surface (and lacks cell surfaceexpression of any endogenous MHC I and MHC II) displays essentiallynormal B to T cell ratio, e.g., B to T cell ratio in the spleen. In someembodiments of the invention, the mouse described herein displays normalT and B cell development, expression levels, and expression patterns. Insome embodiments of the invention, the mouse described herein expresseschimeric human/mouse MHC II only on antigen presenting cells of themouse. In some embodiments, a mouse described herein elicits an immuneresponse, e.g., a cellular immune response, to one or more humanantigens. In some embodiments, a mouse described herein elicits a T cellresponse to one or more human antigens.

In various embodiments, the genetically modified non-human animalsdescribed herein make cells, e.g., APCs, with human or humanized MHC Iand II on the cell surface and, as a result, present peptides asepitopes for T cells in a human-like manner, because substantially allof the components of the complex are human or humanized. The geneticallymodified non-human animals of the invention can be used to study thefunction of a human immune system in the humanized animal; foridentification of antigens and antigen epitopes that elicit immuneresponse (e.g., T cell epitopes, e.g., unique human cancer epitopes),e.g., for use in vaccine development; for evaluation of vaccinecandidates and other vaccine strategies; for studying humanautoimmunity; for studying human infectious diseases; and otherwise fordevising better therapeutic strategies based on human MHC expression.

EXAMPLES

The invention will be further illustrated by the following nonlimitingexamples. These Examples are set forth to aid in the understanding ofthe invention but are not intended to, and should not be construed to,limit its scope in any way. The Examples do not include detaileddescriptions of conventional methods that would be well known to thoseof ordinary skill in the art (molecular cloning techniques, etc.).Unless indicated otherwise, parts are parts by weight, molecular weightis average molecular weight, temperature is indicated in Celsius, andpressure is at or near atmospheric.

Example 1 Engineering a Mouse Comprising Humanized MHC I and MHC II Loci

The various steps involved in engineering a mouse comprising humanizedMHC I and MHC II loci, with corresponding and additional endogenous MHCI and MHC II loci deletions (HLA-A2/H-2K, HLA-DR2/H-2E, H-2A-del,H-2D-del) are depicted in FIG. 4. Detailed description of the stepsappears below.

Example 1.1 Engineering Mouse ES Cells Comprising Humanized MHC I Gene

The mouse H-2K gene was humanized in a single step by construction of aunique targeting vector from human and mouse bacterial artificialchromosome (BAC) DNA using VELOCIGENE® technology (see, e.g., U.S. Pat.No. 6,586,251 and Valenzuela et al. (2003) High-throughput engineeringof the mouse genome coupled with high-resolution expression analysis.Nat. Biotech. 21(6): 652-659). DNA from mouse BAC clone RP23-173k21(Invitrogen) was modified by homologous recombination to replace thegenomic DNA encoding the α1, α2 and α3 domains of the mouse H-2K genewith human genomic DNA encoding the α1, α2 and α3 subunits of the humanHLA-A2 gene (FIG. 5). Detailed steps for construction of BAC DNA can befound in U.S. Patent Application Publication No. 2013-0111617,incorporated herein by reference. The targeted BAC DNA was used toelectroporate mouse F1H4 ES cells to create modified ES cells forgenerating mice that express a chimeric MHC class I protein on thesurface of nucleated cells (e.g., T and B lymphocytes, macrophages,neutrophils). ES cells containing an insertion of human HLA sequenceswere identified by a the quantitative PCR assay using TAQMAN™ (Lie andPetropoulos (1998) Curr. Opin. Biotechnology 9:43-48). Detailed stepsfor construction of mouse ES cells comprising humanized MHC I gene aswell as screening can be also found in the same U.S. Patent ApplicationPublication No. 2013-0111617.

ES cells comprising the chimeric HLA-A2/H-2K were utilized in furthergenetic engineering steps detailed below and in FIG. 4.

Example 1.2 Engineering Mouse ES Cells Comprising Deletion of MHC IILoci

The targeting vector for introducing a deletion of the endogenous MHCclass II H-2Ab1, H-2Aa, H-2Eb1, H-2Eb2, and H-2Ea genes was made usingVELOCIGENE® genetic engineering technology (see, e.g., U.S. Pat. No.6,586,251 and Valenzuela et al., supra). Bacterial Artificial Chromosome(BAC) RP23-458i22 (Invitrogen) DNA was modified to delete the endogenousMHC class II genes H-2Ab1, H-2Aa, H-2Eb1, H-2Eb2, and H-2Ea.

Briefly, upstream and downstream homology arms were derived by PCR ofmouse BAC DNA from locations 5′ of the H-2Ab1 gene and 3′ of the H-2Eagene, respectively. These homology arms were used to make a cassettethat deleted ˜79 kb of RP23-458i22 comprising genes H-2Ab1, H-2Aa,H-2Eb1, H-2Eb2, and H-2Ea of the MHC class II locus by bacterialhomologous recombination (BHR). This region was replaced with a neomycincassette flanked by lox2372 sites. The final targeting vector includedfrom 5′ to 3′ a 26 kb homology arm comprising mouse genomic sequence 5′to the H-2Ab1 gene of the endogenous MHC class II locus, a 5′ lox2372site, a neomycin cassette, a 3′ lox2372 site and a 63 kb homology armcomprising mouse genomic sequence 3′ to the H-2Ea gene of the endogenousMHC class II locus (MAID 5092).

The BAC DNA targeting vector (described above) was used to electroporatemouse ES cells comprising humanized MHC I locus (from Example 1.1 above)to create modified ES cells comprising a deletion of the endogenous MHCclass II locus (both H-2A and H-2E were deleted). Positive ES cellscontaining a deleted endogenous MHC class II locus were identified bythe quantitative PCR assay using TAQMAN™ probes (Lie and Petropoulos(1998) Curr. Opin. Biotechnology 9:43-48). The upstream region of thedeleted locus was confirmed by PCR using primers 5111U F(CAGAACGCCAGGCTGTAAC; SEQ ID NO:1) and 5111U R (GGAGAGCAGGGTCAGTCAAC;SEQ ID NO:2) and probe 5111U P (CACCGCCACTCACAGCTCCTTACA; SEQ ID NO:3),whereas the downstream region of the deleted locus was confirmed usingprimers 5111D F (GTGGGCACCATCTTCATCATTC; SEQ ID NO:4) and 5111D R(CTTCCTTTCCAGGGTGTGACTC; SEQ ID NO:5) and probe 5111D P(AGGCCTGCGATCAGGTGGCACCT; SEQ ID NO:6). The presence of the neomycincassette from the targeting vector was confirmed using primers NEOF(GGTGGAGAGGCTATTCGGC; SEQ ID NO:7) and NEOR (GAACACGGCGGCATCAG; SEQ IDNO:8) and probe NEOP (TGGGCACAACAGACAATCGGCTG; SEQ ID NO:9). Thenucleotide sequence across the upstream deletion point (SEQ ID NO:10)included the following, which indicates endogenous mouse sequenceupstream of the deletion point (contained within the parentheses below)linked contiguously to cassette sequence present at the deletion point:(TTTGTAAACA AAGTCTACCC AGAGACAGAT GACAGACTTC AGCTCCAATG CTGATTGGTTCCTCACTTGG GACCAACCCT) ACCGGTATAA CTTCGTATAA GGTATCCTAT ACGAAGTTATATGCATGGCC TCCGCGCCGG. The nucleotide sequence across the downstreamdeletion point (SEQ ID NO:11) included the following, which indicatescassette sequence contiguous with endogenous mouse sequence downstreamof the deletion point (contained within the parentheses below):CGACCTGCAG CCGGCGCGCC ATAACTTCGT ATAAGGTATC CTATACGAAG TTATCTCGAG(CACAGGCATT TGGGTGGGCA GGGATGGACG GTGACTGGGA CAATCGGGAT GGAAGAGCATAGAATGGGAG TTAGGGAAGA).

Subsequently to generation of the ES cells comprising both the MHC Ihumanization and endogenous MHC II deletion described above, the loxedneomycin cassette was removed using CRE. Specifically, a plasmidencoding Cre recombinase was electroporated into ES cells to remove theneomycin cassette.

Example 1.3 Generation of Mouse ES Cells Comprising H2-D Locus Deletion

To delete mouse H-2D locus, BHR was used to modify mouse BAC clonebMQ-218H21 (Sanger Institute), replacing 3756 bp of the H2-D gene (fromthe ATG start codon to 3 bp downstream of the TGA stop codon, exons 1-8of mouse H-2D) with a 6,085 bp cassette containing from 5′ to 3′: a LacZgene in frame with a 5′ loxp site, UbC promoter, Neomycin gene, and 3′loxp site.

The BAC DNA targeting vector (described above) was used to electroporatemouse ES cells comprising humanized MHC I locus and a deletion of mouseMHC II, described in Example 1.2 above. Positive ES cells containing adeleted endogenous H-2D locus were identified by the quantitative PCRassay, as described above. Table 1 contains primers and probes used forthe quantitative PCR assay.

TABLE 1 TAQMAN ™ Loss of Allele Assay Primers and Probes Name ForwardReverse (location) Primer Primer Probe 5152 mTU CGAGGAGCC AAGCGCACGACTCTGTCGG (upstream) CCGGTACA ACTCCTTGTT CTATGTGG (SEQ ID (SEQ ID(SEQ ID NO: 12) NO: 13) NO: 14) 5152 mTD GGACTCCCAGA GAGTCATGAACCATGGTGGGT (downstream) ATCTCCTGAGA TCACTGTGAAGA TGCTGGAA (SEQ ID (SEQ ID(SEQ ID NO: 15) NO: 16) NO: 17)

Example 1.4 Generation of Mouse ES Cells Comprising Humanized MHC IILocus

To generate a vector comprising humanized HLA-DR2/H-2E, first, mouseH-2Ea gene was modified in accordance with the description in US PatentApplication Publication No. US 2013-0111616, incorporated herein byreference, to generate a vector comprising sequence encoding a chimericH-2Ea/HLA-DRA1*01 protein.

For mouse H-2Eb gene, synthesized human HLA-DR2 β chain (DRB1*1501) wasused to generate a vector comprising DRβ1*02(1501) exons and introns,and swapped using bacterial homologous recombination into the vectorcomprising chimeric H-2Ea/HLA-DRA1*01 protein. H-2Eb gene was modifiedessentially as described in U.S. Patent Application Publication Nos. US2013-0111616 and US 2013-0185820, incorporated herein by reference. Ahygromycin selection cassette was used.

The resulting HLA-DR2/H-2E LTVEC is depicted in FIG. 6. The variousnucleotide sequence junctions of the resulting LTVECs (e.g., mouse/humansequence junctions, human/mouse sequence junctions, or junctions ofmouse or human sequence with selection cassettes) are summarized belowin Table 2 and listed in the Sequence Listing; their locations areindicated in the schematic diagram of FIG. 6. In Table 2 below, with theexception of sequences marked with asterisks (*, see Table legend) themouse sequences are in regular font; the human sequences are inparentheses; the Lox sequences are italicized; and the restriction sitesintroduced during cloning steps and other vector-based sequences (e.g.,multiple cloning sites, etc.) are bolded.

TABLE 2 Nucleotide Sequence Junctions SEQ ID NO: Nucleotide Sequence 18CTGTTTCTTC CCTAACTCCC ATTCTATGCT CTTCCATCCC GA CCGCGG (CCCA ATCTCTCTCC ACTACTTCCT GCCTACATGT ATGTAGGT) 19(CAAGGTTTCC TCCTATGATG CTTGTGTGAA ACTCGG)GGCC GGCC AGCATTTAAC AGTACAGGGA TGGGAGCACA GCTCAC  20*(GAAAGCAGTC TTCCCAGCCT TCACACTCAG AGGTACAAAT) CCCCATTTTC ATATTAGCGA TTTTAATTTA TTCTAGCCTC  21*TCTTCCCTAA CTCCCATTCT ATGCTCTTCC ATCCCGACCG CGG (CCCAATC TCTCTCCACT ACTTCCTGCC TACATGTATG) 22GAGTTCCTCCATCACTTCACTGGGTAGCACAGCTGTAACTGTCCAGCCTG(TCCTGGGCTGCAGGTGGTGGGCGTTGCGGGT GGGGCCGGTTAAGGTTCCA) 23(TCCCACATCCTATTTTAATTTGCTCCATGTTCTCATCTCCATCAGCACAG)CTCGAG ATAACTTCGTATAATGTATGCTA TACGAAGTTAT ATGCATGGCC 24ATACGAAGTTAT GCTAGTAACTATAACGGTCCTAAGGTAGCGAGTGGCTT ACAGGTAGGTGCGTGAAGCTTCTACAAGCA CAGTTGCCCCCTGGGAAGCA*Sequences marked with asterisk are C57BL/6-BALB/c junction sequenceswhere C57BL/6 sequences are in parentheses. During cloning of thechimeric H-2Ea gene, exon 1 and the remainder of intron 1 of the C57BL/6allele of H-2Ea was replaced with the equivalent 2616 bp region from theBALB/c allele of H-2Ea. This was done because exon 1 of the C57BL/6allele of H-2Ea contains a deletion which renders the genenonfunctional, while exon 1 of BALB/c allele of H-2Ea is functional. Fora more detailed description, see U.S. Patent Application Publication No.US 2013-0111616, incorporated herein by reference.

The targeted BAC DNA described above was used to electroporate mouse EScells comprising humanized MHC I (HLA-A2), as well as MHC II and H-2Ddeletion to create modified ES cells for generating mice that expresschimeric MHC I and MHC II genes and lack functional endogenous mouseH-2E, H-2A, H-2K, and H-2D loci. ES cells containing an insertion ofhuman HLA sequences were identified by a quantitative PCR (TAQMAN™)assay, using primers and probes in Table 3 and the procedure describedabove.

TABLE 3 TAQMAN ™ Primer and Probe Sequences Name Forward Reverse(location) Primer Primer Probe Hyg cassette TGCGGCCGATC TTGACCGATTCCTACGAGCGGGTT TTAGCC (SEQ TGCGG (SEQ CGGCCCATTC ID NO: 25) ID NO: 26)(SEQ ID NO: 27) 7092 hTUP1 CCCCACAGCAC CGTCCCATTGAAG TGGCAGCCTAA(Exon 2 of GTTTCCT AAATGACACT GAGG (SEQ DRB1*1501) (SEQ ID NO:(SEQ ID NO: ID NO: 30) 28) 29) 7092 hTUP2 CCCCACAGCAC ACCCGCTCCGTCCAGCCTAAGAGG (Exon 2 of GTTTCCT CATT GAGTGTC DRB1*1501) (SEQ ID NO:(SEQ ID NO: (SEQ ID NO: 31) 32) 33) 7092 hTDP1 AGACCCTGGTG CGCTTGGGTGCTCTCGAAGTGGAG (Exon 3 of ATGCTGGAA CACTT AGGTTTA DRB1*1501) (SEQ ID NO:(SEQ ID NO: (SEQ ID NO: 34) 35) 36) 7092 hTDP2 TGGAATGGAGT GCACGGTCCCCTTTGACTTCCTAA (exon 3 of GAGCAGCTTT CTTAGTG ATTTCTC DRB1*1501) (SEQ ID NO:(SEQ ID NO: (SEQ ID NO: 37) 38) 39) hDRAIU CTGGCGGCTTG CATGATTTCCAGGCGATTTGCCAG (exon 2 of AAGAATTTGG TTGGCTTTGTC CTTTGAGGCTC DRA)(SEQ ID NO: (SEQ ID NO: AAGG (SEQ 40) 41) ID NO: 42) 1751jxn2¹CCTCACTTGGG TTGTCCCAGTCAC TGCATCTCGAG (loss-of- ACCAACCCTA CGTCCATCACAGGCATTT allele assay, (SEQ ID NO: (SEQ ID NO: GG (SEQ sequence 43)44) ID NO: 45) present in H- 2A and H-2E delete only) ¹All sequencesexcept this one are used in the gain-of-allele assay.

The selection cassette may be removed by methods known by the skilledartisan. For example, ES cells bearing the chimeric human/mouse MHCclass I locus may be transfected with a construct that expresses Cre inorder to remove the “loxed” selection cassette introduced by theinsertion of the targeting construct. The selection cassette mayoptionally be removed by breeding to mice that express Cre recombinase.Optionally, the selection cassette is retained in the mice.

Targeted ES cells containing all of the modifications described inExamples 1.1-1.4 (H2-K^(+/1666) MHC-II^(+/6112) H2-D^(+/delete) of FIG.4) were verified using a quantitative TAQMAN® assay described aboveusing the primer/probe sets described herein for individualmodifications. An additional primer/probe set was used to determine thatduring cassette-deletion step, no inverted clone was created due to loxsites present in opposing orientation.

Targeted ES cells described above were used as donor ES cells andintroduced into an 8-cell stage mouse embryo by the VELOCIMOUSE® method(see, e.g., U.S. Pat. No. 7,294,754 and Poueymirou et al. (2007) F0generation mice that are essentially fully derived from the donorgene-targeted ES cells allowing immediate phenotypic analyses NatureBiotech. 25(1):91-99). VELOCIMICE® (F0 mice fully derived from the donorES cell) independently bearing a chimeric MHC class I and MHC II geneswere identified by genotyping using a modification of allele assay(Valenzuela et al., supra) that detects the presence of the unique humangene sequences. A schematic representation of the genotype of MHC lociin the resulting mice is depicted in FIG. 7 (** represents H-2L genewhich is not present in all mouse strains).

Example 1.5 Characterization of Mice Comprising Chimeric MHC I and IIGenes

Spleens from WT or heterozygous humanized HLA-A2/HLA-DR2/H-2D-del mice(see mice generated on the bottom of FIG. 4 (“HLA-A2/H-2K, HLA-DR2/H-2E,H-2A-del, H-2D-del HET” or “H-2K^(+/1666) MHC-II^(+/6112)H2-D^(+/delete)” or “chimeric A2 and DR2”) were harvested, and singlecell suspensions were prepared. Cell surface expression of mouse MHCclass I (H2D), human MHC class I (HLA-A2), and human MHC class II(HLA-DR) on CD3+T cells, CD19+B cells, and CD14+ monocytes were analyzedby FACS. As shown in FIG. 8, there was no significant disruption in T toB cell ratio or no significant effect on T and B cell development.Expression of human HLA-A2 and HLA-DR were detectable on the surface ofCD19+B cells and monocytes (FIGS. 9 and 10). Expression of human HLA-A2,but not HLA-DR, was detectable on the surface of CD3+T cells (FIG. 11),as MHC II is only expressed on antigen-presenting cells.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents of the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

Entire contents of all non-patent documents, patent applications andpatents cited throughout this application are incorporated by referenceherein in their entirety.

What is claimed is:
 1. A non-human animal comprising at an endogenousMHC locus: a first nucleotide sequence encoding a chimerichuman/non-human animal MHC I polypeptide, wherein a human portion of thechimeric MHC I polypeptide comprises an extracellular domain of a humanMHC I polypeptide, a second nucleotide sequence encoding a chimerichuman/non-human animal MHC II α polypeptide, wherein a human portion ofthe chimeric human/non-human MHC II α polypeptide comprises anextracellular domain of a human MHC II α polypeptide, and a thirdnucleotide sequence encoding a chimeric human/non-human animal MHC II βpolypeptide, wherein a human portion of the chimeric human/non-human MHCII β polypeptide comprises an extracellular domain of a human MHC II βpolypeptide, wherein the non-human animal expresses chimerichuman/non-human MHC I and MHC II proteins from the endogenous MHC locus,and wherein all genes encoding endogenous non-human animal MHC I and MHCII proteins that are expressed on a cell surface are functionallyinactivated.
 2. The non-human animal of claim 1, wherein the firstnucleotide sequence is located at an endogenous non-human animal MHC Ilocus, the second nucleotide sequence is located at an endogenousnon-human animal MHC II α locus, and the third nucleotide sequence islocated at an endogenous non-human animal MHC II β locus.
 3. Thenon-human animal of claim 1, wherein the first, second and/or thirdnucleotide sequence(s) are operably linked to endogenous non-humananimal regulatory elements.
 4. The non-human animal of claim 1, whereinthe human portion of the chimeric MHC I polypeptide comprises α1, α2,and α3 domains of the human MHC I polypeptide.
 5. The non-human animalof claim 1, wherein the non-human animal portion of the chimeric MHC Ipolypeptide comprises transmembrane and cytoplasmic domains of anendogenous non-human MHC I polypeptide.
 6. The non-human animal of claim1, wherein the human MHC I polypeptide is selected from the groupconsisting of HLA-A, HLA-B, and HLA-C.
 7. The non-human animal of claim1, further comprising at an endogenous non-human animal β2 microglobulinlocus a nucleotide sequence encoding a human or humanized β2microglobulin polypeptide, wherein the non-human animal expresses thehuman or humanized β2 microglobulin polypeptide.
 8. The non-human animalof claim 1, wherein the human MHC II α extracellular domain compriseshuman MHC II α1 and α2 domains.
 9. The non-human animal of claim 1,wherein the human MHC II β extracellular domain comprises human MHC IIβ1 and β2 domains.
 10. The non-human animal of claim 1, wherein thefirst nucleotide sequence is operably linked to endogenous non-humananimal MHC I promoter and regulatory elements, the second nucleotidesequence is operably linked to endogenous non-human animal MHC II αpromoter and regulatory elements, and the third nucleotide sequence isoperably linked to endogenous non-human animal MHC II β promoter andregulatory elements.
 11. The non-human animal of claim 1, wherein thenon-human animal portion of the chimeric human/non-human animal MHC II αpolypeptide comprises transmembrane and cytoplasmic domains of anendogenous non-human animal MHC II α polypeptide.
 12. The r non-humananimal of claim 1, wherein the non-human animal portion of the chimerichuman/non-human animal MHC II β polypeptide comprises transmembrane andcytoplasmic domains of an endogenous non-human animal MHC II βpolypeptide.
 13. The non-human animal of claim 1, wherein the humanportions of the chimeric human/non-human animal MHC II α and βpolypeptides are derived from a human HLA class II protein selected fromthe group consisting of HLA-DR, HLA-DQ, and HLA-DP.
 14. The non-humananimal of claim 13, wherein the human portions of the chimerichuman/non-human animal MHC II α and β polypeptides are derived from ahuman HLA-DR protein.
 15. The non-human animal of claim 1, wherein thenon-human animal is a mouse, wherein the first nucleotide sequenceencodes a chimeric human/mouse MHC I polypeptide, and wherein a mouseportion of the chimeric MHC I polypeptide is derived from H-2K, H-2D, orH-2L.
 16. The mouse of claim 15, wherein the mouse portion of thechimeric MHC I polypeptide is derived from H-2K.
 17. The non-humananimal of claim 13, wherein the non-human animal is a mouse, wherein thesecond nucleotide sequence encodes a chimeric human/mouse MHC II αpolypeptide, the third nucleotide sequence encodes a chimerichuman/mouse MHC II β polypeptide, and wherein mouse portions of thechimeric MHC II α and β polypeptides are derived from H-2E or H-2A. 18.The mouse of claim 17, wherein the mouse portions of the chimeric MHC IIpolypeptides are derived from H-2E.
 19. The mouse of claim 18, whereinthe mouse endogenous gene encoding a H-2A polypeptide is functionallyinactivated.
 20. The non-human animal of claim 1, wherein the non-humananimal is a mouse, wherein the first nucleotide sequence encodes achimeric HLA-A/H-2K polypeptide, the second nucleotide sequence encodesan α chain of a chimeric HLA-DR/H-2E polypeptide, and the thirdnucleotide sequence encodes a β chain of a chimeric HLA-DR/H-2Epolypeptide, and wherein the mouse expresses HLA-A/H-2K and HLA-DR/H-2Eproteins.
 21. The mouse of claim 20, wherein the first nucleotidesequence is located at an endogenous mouse H-2K locus and wherein themouse lacks all or part of an endogenous H-2D gene and/or all or part ofan endogenous mouse H-2L gene.
 22. The mouse of claim 20, wherein thesecond nucleotide sequence is located at an endogenous H-2E α locus andthe third nucleotide sequence is located at an endogenous H-2E β gene,and wherein the mouse lacks all or part of an endogenous mouse H-2Agene.
 23. The mouse of claim 21, wherein the second nucleotide sequenceis located at an endogenous H-2E α locus and the third nucleotidesequence is located at an endogenous H-2E β locus, and wherein the mouselacks all or part of an endogenous mouse H-2A gene.
 24. The non-humananimal of claim 1, wherein the non-human animal is a rodent.
 25. Thenon-human animal of claim 23, wherein the rodent is a mouse or a rat.